Variant report

Variant	rs7609904
Chromosome Location	chr3:112130589-112130590
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	ESR1	chr3:112130334-112130639	ECC-1	luminal epithelium:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
2	ESR1	chr3:112130266-112130771	ECC-1	luminal epithelium:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
3	MAX	chr3:112130438-112130655	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr3:112130334-112130660	HepG2	liver:	n/a	n/a
5	ESR1	chr3:112130277-112130757	ECC-1	luminal epithelium:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
6	ESR1	chr3:112130310-112130693	T-47D	breast:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
7	ESR1	chr3:112130298-112130707	T-47D	breast:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
8	ESR1	chr3:112130353-112130691	ECC-1	luminal epithelium:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
9	ESR1	chr3:112130302-112130699	T-47D	breast:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
10	ESR1	chr3:112130292-112130656	T-47D	breast:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539
11	ESR1	chr3:112130357-112130647	T-47D	breast:	n/a	chr3:112130523-112130540 chr3:112130523-112130538 chr3:112130522-112130539

Variant related genes	Relation type
ENSG00000243081	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10511310	1.00[CHB][hapmap]
rs10804498	1.00[ASN][1000 genomes]
rs10934163	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10934164	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10934165	1.00[ASN][1000 genomes]
rs11709101	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712849	1.00[ASN][1000 genomes]
rs11717777	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720514	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923402	1.00[ASN][1000 genomes]
rs11926389	1.00[CHB][hapmap]
rs12489616	1.00[CHB][hapmap]
rs12497979	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13063452	1.00[CHB][hapmap]
rs13064242	1.00[CHB][hapmap]
rs13084103	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1317295	1.00[ASN][1000 genomes]
rs1317658	1.00[ASN][1000 genomes]
rs13316383	1.00[ASN][1000 genomes]
rs1388858	1.00[CHB][hapmap]
rs1388859	1.00[CHB][hapmap]
rs17235534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17446282	1.00[CHB][hapmap]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2633546	1.00[ASN][1000 genomes]
rs2683891	1.00[ASN][1000 genomes]
rs2683892	1.00[ASN][1000 genomes]
rs28615303	1.00[ASN][1000 genomes]
rs4234411	1.00[CHB][hapmap]
rs4321508	1.00[CHB][hapmap]
rs4347976	1.00[CHB][hapmap]
rs4507229	1.00[ASN][1000 genomes]
rs4538347	1.00[CHB][hapmap]
rs4622877	1.00[ASN][1000 genomes]
rs4638935	1.00[CHB][hapmap]
rs4682393	1.00[ASN][1000 genomes]
rs4682400	1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	1.00[ASN][1000 genomes]
rs56008438	1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[ASN][1000 genomes]
rs60949597	1.00[ASN][1000 genomes]
rs62262366	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262408	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262411	1.00[ASN][1000 genomes]
rs62262459	1.00[ASN][1000 genomes]
rs62264125	1.00[ASN][1000 genomes]
rs62264128	1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	1.00[ASN][1000 genomes]
rs62278768	1.00[ASN][1000 genomes]
rs62278769	1.00[ASN][1000 genomes]
rs62278770	1.00[ASN][1000 genomes]
rs62278771	1.00[ASN][1000 genomes]
rs62278843	1.00[ASN][1000 genomes]
rs6438072	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6787323	1.00[CHB][hapmap]
rs6789875	1.00[CHB][hapmap]
rs6795820	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6804836	1.00[CHB][hapmap]
rs6805112	1.00[CHB][hapmap]
rs73223638	1.00[ASN][1000 genomes]
rs7431999	1.00[CHB][hapmap]
rs7612748	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7621431	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7631673	1.00[ASN][1000 genomes]
rs7636107	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7637676	1.00[CHB][hapmap]
rs7650962	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651121	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288939	1.00[CHB][hapmap]
rs9288942	1.00[CHB][hapmap]
rs9810421	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9816969	1.00[ASN][1000 genomes]
rs9818407	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	1.00[ASN][1000 genomes]
rs9851760	1.00[ASN][1000 genomes]
rs9853669	1.00[ASN][1000 genomes]
rs9855755	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]
rs9871492	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002567	chr3:112088498-112144063	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv2830128	chr3:112090292-112144026	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv997659	chr3:112099148-112135687	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7609904	BTLA	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112125400-112132200	Weak transcription	Placenta	Placenta
2	chr3:112126200-112134000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:112126200-112134400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:112126200-112135200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:112126400-112134200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:112126600-112135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:112126600-112135400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:112126800-112131600	Weak transcription	Primary B cells from cord blood	blood
9	chr3:112126800-112135200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:112126800-112136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:112127000-112131600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:112128200-112132200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:112128800-112132600	Weak transcription	Fetal Intestine Large	intestine
14	chr3:112129200-112132200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:112129600-112130800	Enhancers	Aorta	Aorta
16	chr3:112130000-112130600	Enhancers	Fetal Heart	heart
17	chr3:112130000-112130800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:112130000-112130800	Enhancers	HSMMtube	muscle
19	chr3:112130200-112130600	Enhancers	Left Ventricle	heart
20	chr3:112130400-112130600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:112130400-112130800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:112130400-112130800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr3:112130400-112130800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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