Variant report

Variant	rs11053060
Chromosome Location	chr12:34176861-34176862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:33590585..33592422-chr12:34176176..34177683,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10844772	0.82[JPT][hapmap]
rs10844775	0.82[JPT][hapmap]
rs10844776	0.82[JPT][hapmap]
rs10844777	0.82[JPT][hapmap]
rs10844839	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs11053023	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11053026	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11053035	0.82[JPT][hapmap]
rs11053046	0.82[JPT][hapmap]
rs11053061	0.82[JPT][hapmap]
rs12049938	0.82[JPT][hapmap]
rs1619785	0.82[JPT][hapmap]
rs3655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs366873	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558247	chr12:33481504-34245756	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1037735	chr12:33510115-34457196	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv469348	chr12:33524082-34245756	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv558249	chr12:33524082-34245756	Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1047430	chr12:33526355-34435009	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv1040037	chr12:33526355-34457196	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	nsv1049273	chr12:33528203-34491300	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv541462	chr12:33528203-34491300	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1042712	chr12:33528204-34427733	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv541463	chr12:33528204-34427733	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1047392	chr12:33528403-34427593	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv541464	chr12:33528403-34427593	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv1051183	chr12:33528403-34491152	Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
14	nsv541465	chr12:33528403-34491152	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv469350	chr12:33752330-34245756	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	nsv558295	chr12:33752330-34245756	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	nsv534000	chr12:33822185-34756209	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
18	esv2830231	chr12:33826241-34801271	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
19	nsv1040812	chr12:33863411-34854486	Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
20	nsv1051316	chr12:33956561-34428933	Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
21	nsv1051986	chr12:33962656-34457196	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
22	nsv917816	chr12:33967852-34854486	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
23	nsv1044382	chr12:33968178-34854486	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
24	nsv558297	chr12:34020094-34757810	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	nsv533940	chr12:34023331-34756209	Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
26	nsv1045677	chr12:34024348-34854486	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
27	nsv1043754	chr12:34030026-34435009	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
28	nsv1037287	chr12:34030936-34491152	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
29	nsv541471	chr12:34030936-34491152	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
30	nsv915754	chr12:34052409-34756196	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
31	nsv430503	chr12:34059018-34760333	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
32	nsv558298	chr12:34081127-34245756	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
33	nsv558299	chr12:34081127-34252870	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
34	nsv918189	chr12:34089213-34854486	Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
35	nsv1038502	chr12:34110609-34787964	Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
36	nsv520568	chr12:34111494-34436391	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
37	nsv527701	chr12:34111494-34819926	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
38	nsv1045139	chr12:34125978-34854486	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
39	nsv1036399	chr12:34160024-34854486	ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
40	nsv983459	chr12:34173918-34178625	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11053060	SEMA4A	trans	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:34174600-34177000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:34175800-34184200	Weak transcription	Spleen	Spleen
3	chr12:34176000-34177000	Flanking Active TSS	Dnd41	blood
4	chr12:34176000-34178800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:34176000-34179000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:34176000-34186800	Weak transcription	Lung	lung
7	chr12:34176200-34177000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:34176200-34177000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:34176200-34177000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr12:34176200-34177000	Enhancers	Liver	Liver
11	chr12:34176200-34177000	Enhancers	Fetal Lung	lung
12	chr12:34176200-34177000	Enhancers	Fetal Stomach	stomach
13	chr12:34176200-34177000	Enhancers	HUVEC	blood vessel
14	chr12:34176200-34177200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:34176200-34177400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:34176200-34177600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:34176200-34177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:34176200-34177800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:34176200-34178400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:34176200-34178400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:34176200-34178400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:34176200-34178400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:34176200-34178400	Weak transcription	Fetal Brain Female	brain
24	chr12:34176200-34178600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:34176200-34178800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:34176200-34178800	Weak transcription	Thymus	Thymus
27	chr12:34176200-34178800	Weak transcription	Hela-S3	cervix
28	chr12:34176200-34179200	Weak transcription	Fetal Intestine Large	intestine
29	chr12:34176200-34179800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:34176200-34179800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:34176200-34179800	Weak transcription	HSMM	muscle
32	chr12:34176200-34180000	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:34176200-34180000	Weak transcription	Left Ventricle	heart
34	chr12:34176200-34180000	Weak transcription	NHDF-Ad	bronchial
35	chr12:34176200-34181200	Weak transcription	Fetal Thymus	thymus
36	chr12:34176200-34182200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:34176200-34182400	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:34176200-34182400	Weak transcription	Brain Substantia Nigra	brain
39	chr12:34176200-34182400	Weak transcription	Right Ventricle	heart
40	chr12:34176200-34182600	Weak transcription	Pancreas	Pancrea
41	chr12:34176200-34182800	Weak transcription	Gastric	stomach
42	chr12:34176200-34183200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:34176200-34184200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:34176200-34184200	Weak transcription	Esophagus	oesophagus
45	chr12:34176200-34184800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:34176200-34187200	Weak transcription	Ovary	ovary
47	chr12:34176400-34177000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:34176400-34177000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr12:34176400-34177000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr12:34176400-34177200	Enhancers	NHEK	skin

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