Variant report

Variant	rs12278108
Chromosome Location	chr11:75066489-75066490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr11:75066167-75066616	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr11:75065953-75066586	ECC-1	luminal epithelium:	n/a	n/a
3	USF1	chr11:75066141-75066599	ECC-1	luminal epithelium:	n/a	n/a
4	NFIC	chr11:75065878-75066607	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr11:75065924-75066626	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr11:75065983-75066728	ECC-1	luminal epithelium:	n/a	n/a
7	YY1	chr11:75066077-75066636	ECC-1	luminal epithelium:	n/a	n/a
8	USF2	chr11:75066422-75066515	Hela-S3	cervix:	n/a	n/a
9	NFIC	chr11:75065990-75066584	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr11:75065956-75066605	ECC-1	luminal epithelium:	n/a	n/a
11	USF1	chr11:75066367-75066590	K562	blood:	n/a	n/a
12	MAX	chr11:75066054-75066613	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:75061810..75065838-chr11:75066153..75069996,4	MCF-7	breast:
2	chr11:75011382..75013616-chr11:75065384..75067528,2	MCF-7	breast:
3	chr11:75065936..75068463-chr11:75068645..75070545,2	K562	blood:

No data

Variant related genes	Relation type
ARRB1	TF binding region
ENSG00000137486	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10899087	0.95[ASN][1000 genomes]
rs11236397	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236398	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11236401	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236405	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11236407	0.85[CEU][hapmap]
rs11236416	0.88[AMR][1000 genomes]
rs11602596	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605734	0.82[AMR][1000 genomes]
rs12269895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12270766	0.88[AMR][1000 genomes]
rs12271518	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12271945	0.93[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes]
rs12283536	0.82[AMR][1000 genomes]
rs12291595	0.93[CEU][hapmap];0.88[AMR][1000 genomes]
rs12577286	0.95[ASN][1000 genomes]
rs12790302	0.82[AMR][1000 genomes]
rs12794577	0.88[AMR][1000 genomes]
rs12797588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34530827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775308	0.82[AMR][1000 genomes]
rs4121885	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7101921	0.85[AMR][1000 genomes]
rs7116977	0.85[AMR][1000 genomes]
rs7120396	0.93[CEU][hapmap];0.85[AMR][1000 genomes]
rs7131065	0.82[AMR][1000 genomes]
rs73004237	0.85[AMR][1000 genomes]
rs7929742	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
2	nsv832211	chr11:74945839-75106125	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
3	nsv522447	chr11:74982939-75068767	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12278108	GDPD4	cis	cerebellum	SCAN
rs12278108	C2CD3	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75063400-75067600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:75063600-75076800	Weak transcription	Hela-S3	cervix
3	chr11:75063800-75067000	Weak transcription	HMEC	breast
4	chr11:75063800-75067400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr11:75064000-75067400	Weak transcription	HSMM	muscle
6	chr11:75064000-75067600	Weak transcription	HSMMtube	muscle
7	chr11:75064000-75067600	Weak transcription	NHDF-Ad	bronchial
8	chr11:75064200-75066800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr11:75064200-75067400	Weak transcription	HUVEC	blood vessel
10	chr11:75064200-75067600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:75064200-75067600	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:75064200-75068200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr11:75064200-75068600	Weak transcription	Small Intestine	intestine
14	chr11:75064200-75086800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:75064400-75066800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr11:75064400-75067000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:75064400-75067000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:75064400-75067600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:75064400-75067600	Weak transcription	Spleen	Spleen
20	chr11:75064600-75067000	Weak transcription	Primary T cells from cord blood	blood
21	chr11:75064600-75067000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:75064600-75071800	Weak transcription	Primary B cells from cord blood	blood
23	chr11:75064800-75066800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:75065400-75066600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr11:75065400-75067200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:75066400-75066600	Enhancers	Gastric	stomach
27	chr11:75066400-75066600	Enhancers	A549	lung
28	chr11:75066400-75066800	Enhancers	Primary T helper cells fromperipheralblood	blood

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