Variant report

Variant	rs11111759
Chromosome Location	chr12:104163183-104163184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr12:104162915-104163261	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr12:104162763-104163420	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:104163042-104163498	K562	blood:	n/a	n/a
4	POLR2A	chr12:104163136-104163234	HepG2	liver:	n/a	n/a
5	MYC	chr12:104162965-104163382	NB4	blood:	n/a	chr12:104163085-104163094
6	USF1	chr12:104162882-104163302	H1-hESC	embryonic stem cell:	n/a	n/a
7	USF1	chr12:104162887-104163340	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr12:104162676-104163411	NB4	blood:	n/a	chr12:104163085-104163094
9	USF1	chr12:104162801-104163293	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104163154..104166859-chr12:104341815..104344175,3	K562	blood:
2	chr12:104156978..104159954-chr12:104162925..104164742,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257681	TF binding region
ENSG00000136011	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10861094	1.00[CEU][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10861095	0.95[CEU][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861096	0.90[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861097	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861098	0.85[AFR][1000 genomes]
rs10861099	0.85[AFR][1000 genomes]
rs11111750	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11111752	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111754	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11111755	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11111757	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11111758	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11111762	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11111763	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11111765	0.90[AMR][1000 genomes]
rs11111767	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11111771	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11111776	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11111778	0.82[AMR][1000 genomes]
rs11111779	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1565773	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs15918	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1866292	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1976256	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2292682	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3751204	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3812805	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4964298	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4964823	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4964827	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4964830	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4981032	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4981036	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs751448	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs869993	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9132	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs934847	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs954920	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899486	chr12:104118587-104170474	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11111759	RP11-341G23.4	cis	Thyroid	GTEx
rs11111759	RP11-341G23.4	cis	Artery Aorta	GTEx
rs11111759	RP11-341G23.4	cis	Artery Tibial	GTEx
rs11111759	RP11-341G23.4	cis	Esophagus Muscularis	GTEx
rs11111759	RP11-341G23.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104145800-104166800	Weak transcription	Right Atrium	heart
2	chr12:104146200-104169400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:104147000-104165400	Strong transcription	Stomach Smooth Muscle	stomach
4	chr12:104150000-104166800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:104151600-104170400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:104152600-104171200	Weak transcription	Esophagus	oesophagus
7	chr12:104152800-104165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:104154800-104170600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:104155000-104169000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:104155000-104170600	Weak transcription	Primary T cells from cord blood	blood
13	chr12:104155000-104170800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:104155000-104171000	Weak transcription	Osteobl	bone
15	chr12:104155000-104178000	Weak transcription	Colonic Mucosa	Colon
16	chr12:104155200-104163200	Weak transcription	NHLF	lung
17	chr12:104155200-104173400	Weak transcription	NHDF-Ad	bronchial
18	chr12:104155800-104169000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:104156000-104170800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:104156200-104170600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:104156600-104166600	Weak transcription	Brain Anterior Caudate	brain
22	chr12:104157400-104166400	Weak transcription	HSMMtube	muscle
23	chr12:104157400-104169000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:104157400-104172400	Weak transcription	GM12878-XiMat	blood
25	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
26	chr12:104157600-104168800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:104157600-104170200	Weak transcription	K562	blood
28	chr12:104157800-104170600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr12:104158200-104170400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:104158600-104170600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:104158600-104170600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:104159000-104166400	Weak transcription	Brain Substantia Nigra	brain
33	chr12:104159200-104170400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:104159400-104170400	Weak transcription	Fetal Brain Female	brain
35	chr12:104160400-104165600	Weak transcription	Gastric	stomach
36	chr12:104160400-104166200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:104160400-104166200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:104160400-104166600	Weak transcription	Fetal Intestine Large	intestine
39	chr12:104160400-104170800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:104160600-104163200	Weak transcription	Lung	lung
42	chr12:104160600-104166200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:104160600-104166200	Weak transcription	Spleen	Spleen
44	chr12:104160600-104166400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:104160600-104170400	Weak transcription	Primary B cells from cord blood	blood
46	chr12:104160600-104170400	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:104160800-104165600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:104160800-104170400	Weak transcription	Placenta	Placenta
49	chr12:104161000-104168800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr12:104161200-104164600	Weak transcription	HSMM	muscle

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