Variant report

Variant	rs11180644
Chromosome Location	chr12:76096630-76096631
allele	A/G
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	TCF7L2	chr12:76095597-76097180	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:76092093..76110851-chr12:76415034..76433496,122	MCF-7	breast:
2	chr12:76094900..76097140-chr12:76097176..76099734,2	K562	blood:
3	chr12:76095482..76097484-chr12:76476603..76478364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258088	TF binding region
ENSG00000257839	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000257453	Chromatin interaction
ENSG00000187109	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11180624	0.82[ASN][1000 genomes]
rs11180639	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11180640	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12315800	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12319659	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12812846	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12822896	0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs12826237	0.83[ASN][1000 genomes]
rs17115480	0.95[CEU][hapmap]
rs17223072	0.83[ASN][1000 genomes]
rs17223194	0.90[CEU][hapmap];0.91[GIH][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs17223651	0.83[ASN][1000 genomes]
rs2367073	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2367074	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34724924	0.87[ASN][1000 genomes]
rs35094428	0.82[ASN][1000 genomes]
rs35813830	0.83[ASN][1000 genomes]
rs35881531	0.95[ASN][1000 genomes]
rs67943440	0.84[ASN][1000 genomes]
rs7132221	0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71460142	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71460144	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295259	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295484	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295806	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7309843	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73124349	0.83[ASN][1000 genomes]
rs7313785	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7967547	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7969436	0.94[CEU][hapmap]
rs7978873	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv899314	chr12:76079814-76110751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11180644	FAM164C	trans	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76076200-76098400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:76079400-76099800	Weak transcription	Right Atrium	heart
3	chr12:76084600-76099600	Weak transcription	Pancreas	Pancrea
4	chr12:76086800-76099400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:76088600-76098600	Weak transcription	NHDF-Ad	bronchial
6	chr12:76088800-76100600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:76089000-76097000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:76089000-76100600	Weak transcription	HMEC	breast
9	chr12:76089200-76098600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:76089600-76099800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:76089600-76100200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:76089600-76100400	Weak transcription	NHEK	skin
13	chr12:76093800-76097000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:76093800-76097200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:76093800-76098000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:76094000-76097000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:76094000-76097200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:76094200-76097200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:76094200-76097200	Weak transcription	Fetal Heart	heart
20	chr12:76094200-76097800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:76094200-76098000	Weak transcription	K562	blood
22	chr12:76094200-76098600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:76094200-76098600	Weak transcription	NHLF	lung
24	chr12:76094200-76098800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:76094200-76098800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:76094200-76099400	Weak transcription	HSMMtube	muscle
27	chr12:76094200-76100200	Weak transcription	Psoas Muscle	Psoas
28	chr12:76095400-76097000	Weak transcription	HUVEC	blood vessel
29	chr12:76095400-76100000	Weak transcription	Adipose Nuclei	Adipose
30	chr12:76095600-76097000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr12:76095600-76097200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:76095600-76097400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:76095800-76097200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:76095800-76097200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:76095800-76097400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:76096000-76100600	Weak transcription	Left Ventricle	heart
37	chr12:76096200-76097400	Enhancers	Primary T cells from cord blood	blood
38	chr12:76096200-76098200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr12:76096400-76096800	Flanking Active TSS	Dnd41	blood

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