Variant report

Variant	rs6775536
Chromosome Location	chr3:112127117-112127118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

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	1.00[ASN][1000 genomes]
rs11712849	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	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[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	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683891	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683892	0.88[EUR][1000 genomes];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	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];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	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]
rs6805397	1.00[CHB][hapmap]
rs73223638	1.00[ASN][1000 genomes]
rs7431999	1.00[CHB][hapmap]
rs7609904	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
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	1.00[ASN][1000 genomes]
rs7651121	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:6 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6775536	BTLA	cis	parietal	SCAN
rs6775536	ATG3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112115200-112127600	Weak transcription	Fetal Kidney	kidney
2	chr3:112118600-112130400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112123800-112128800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:112124800-112127400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:112125400-112130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:112125400-112132200	Weak transcription	Placenta	Placenta
7	chr3:112125800-112127800	Enhancers	Duodenum Mucosa	Duodenum
8	chr3:112126000-112128800	Enhancers	Fetal Intestine Large	intestine
9	chr3:112126200-112134000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:112126200-112134400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:112126200-112135200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:112126400-112134200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:112126600-112135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:112126600-112135400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:112126800-112127200	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr3:112126800-112128600	Weak transcription	Fetal Intestine Small	intestine
17	chr3:112126800-112131600	Weak transcription	Primary B cells from cord blood	blood
18	chr3:112126800-112135200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:112126800-112136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:112127000-112127200	Enhancers	GM12878-XiMat	blood
21	chr3:112127000-112127400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr3:112127000-112131600	Weak transcription	Primary B cells from peripheral blood	blood

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