Variant report

Variant	rs17146121
Chromosome Location	chr11:64386526-64386527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64372156..64374370-chr11:64385204..64388133,2	K562	blood:
2	chr11:64380600..64384034-chr11:64384345..64388589,5	K562	blood:
3	chr11:64382824..64385370-chr11:64385772..64388101,2	MCF-7	breast:
4	chr11:64384619..64387487-chr11:64396791..64398717,2	MCF-7	breast:
5	chr11:64350444..64353414-chr11:64386038..64388659,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10400348	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792444	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10897524	0.81[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10897525	0.88[MEX][hapmap]
rs11231853	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11231859	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11231869	0.88[MEX][hapmap]
rs1143937	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs1207181	0.80[EUR][1000 genomes]
rs12417551	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575704	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1633462	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2003293	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2073798	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs2230414	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2267918	0.89[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2284301	0.89[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2375335	0.81[EUR][1000 genomes]
rs2959652	0.89[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs3741398	0.89[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs3809076	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs474707	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs476037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs477549	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes]
rs483962	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs487105	0.89[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs489192	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs496914	0.89[CEU][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs523200	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs532747	0.82[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs547066	0.92[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs569602	0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs580374	0.84[EUR][1000 genomes]
rs58483071	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs589691	0.89[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap]
rs593394	0.81[EUR][1000 genomes]
rs606458	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs607389	0.89[CEU][hapmap]
rs624975	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs625172	0.93[GIH][hapmap];0.89[MEX][hapmap]
rs637332	0.89[CEU][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs669976	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs677298	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs680273	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs693235	0.80[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs72643567	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72643568	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7939965	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897692	chr11:64305452-64386526	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv897693	chr11:64305452-64440920	Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
8	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
9	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
10	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
11	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
12	nsv897696	chr11:64365796-64412877	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
15	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs17146121	LRRN4CL	cis	cerebellum	SCAN
rs17146121	SF1	cis	lymphoblastoid	seeQTL
rs17146121	TMEM138	cis	parietal	SCAN
rs17146121	EHD1	cis	cerebellum	SCAN
rs17146121	MALAT1	cis	parietal	SCAN
rs17146121	B3GNT1	cis	cerebellum	SCAN
rs17146121	CABP2	cis	parietal	SCAN
rs17146121	TMEM138	cis	cerebellum	SCAN
rs17146121	ANKRD13D	cis	parietal	SCAN
rs17146121	RAB3IL1	cis	parietal	SCAN
rs17146121	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs17146121	PYGM	cis	cerebellum	SCAN
rs17146121	POLA2	cis	cerebellum	SCAN
rs17146121	PYGM	cis	parietal	SCAN
rs17146121	SF1	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64373600-64402200	Weak transcription	HSMMtube	muscle
2	chr11:64376600-64386600	Weak transcription	Right Atrium	heart
3	chr11:64376600-64387000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:64376600-64387200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:64376600-64387200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:64376800-64387200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:64377600-64387000	Strong transcription	Fetal Brain Female	brain
8	chr11:64380000-64387000	Weak transcription	Right Ventricle	heart
9	chr11:64380000-64396800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:64380800-64387000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:64380800-64390800	Weak transcription	Esophagus	oesophagus
12	chr11:64380800-64396600	Weak transcription	NHDF-Ad	bronchial
13	chr11:64382000-64387200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:64382400-64387200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:64382600-64387400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:64382600-64387400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:64382800-64386800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:64382800-64387000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:64382800-64387200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:64382800-64387400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:64383400-64387200	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:64384400-64387000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr11:64384400-64387200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:64384600-64387000	Weak transcription	Fetal Kidney	kidney
25	chr11:64384800-64389400	Weak transcription	HSMM	muscle
26	chr11:64385000-64389600	Weak transcription	Aorta	Aorta
27	chr11:64385200-64387400	Weak transcription	Brain Substantia Nigra	brain
28	chr11:64385200-64389600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr11:64385600-64386800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:64385600-64389800	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr11:64385600-64389800	Enhancers	Pancreas	Pancrea
32	chr11:64385800-64386800	Weak transcription	Fetal Brain Male	brain
33	chr11:64385800-64387400	Enhancers	Liver	Liver
34	chr11:64385800-64389400	Genic enhancers	Fetal Stomach	stomach
35	chr11:64385800-64389800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:64386000-64386600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:64386000-64386800	Enhancers	Fetal Intestine Large	intestine
38	chr11:64386000-64386800	Enhancers	Ovary	ovary
39	chr11:64386000-64387000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:64386000-64387000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr11:64386000-64387000	Weak transcription	Osteobl	bone
42	chr11:64386000-64390800	Enhancers	Fetal Thymus	thymus
43	chr11:64386200-64386600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
44	chr11:64386200-64386600	Weak transcription	Brain Angular Gyrus	brain
45	chr11:64386200-64386600	Genic enhancers	Fetal Intestine Small	intestine
46	chr11:64386200-64386800	Genic enhancers	Brain Germinal Matrix	brain
47	chr11:64386200-64387000	Strong transcription	Brain Cingulate Gyrus	brain
48	chr11:64386200-64389000	Enhancers	Stomach Smooth Muscle	stomach
49	chr11:64386200-64389200	Enhancers	Spleen	Spleen
50	chr11:64386200-64389400	Enhancers	Fetal Lung	lung

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