Variant report

Variant	rs4712981
Chromosome Location	chr6:26361430-26361431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:26360981-26361438	GM12878	blood:	n/a	n/a
2	MAZ	chr6:26361156-26361496	GM12878	blood:	n/a	n/a
3	FOXM1	chr6:26360756-26361495	GM12878	blood:	n/a	n/a
4	RUNX3	chr6:26360620-26361642	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26360907..26362623-chr6:26548003..26549634,2	K562	blood:
2	chr6:26357664..26362871-chr6:26362883..26366982,9	K562	blood:
3	chr6:26360109..26361715-chr6:26372989..26375105,2	K562	blood:
4	chr6:26361147..26363734-chr6:26409271..26412896,3	K562	blood:
5	chr6:26157037..26159929-chr6:26360072..26362483,2	K562	blood:
6	chr6:26360935..26366570-chr6:26520779..26523276,5	K562	blood:
7	chr6:26360935..26364416-chr6:26520779..26522591,4	K562	blood:
8	chr6:26196455..26200961-chr6:26360873..26365378,4	K562	blood:
9	chr6:26361226..26362867-chr6:26363183..26365320,2	MCF-7	breast:

No data

Variant related genes	Relation type
BTN3A2	TF binding region
ENSG00000197409	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000215979	Chromatin interaction
ENSG00000186470	Chromatin interaction
ENSG00000026950	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000228223	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10946813	0.86[GIH][hapmap]
rs10946816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173854	1.00[JPT][hapmap]
rs12174602	1.00[JPT][hapmap]
rs12174631	1.00[JPT][hapmap]
rs12176317	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12199613	0.91[GIH][hapmap]
rs12206621	0.80[YRI][hapmap]
rs13216828	1.00[JPT][hapmap]
rs13218591	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1985732	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073529	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2073531	1.00[JPT][hapmap]
rs2273558	0.82[CEU][hapmap]
rs3734536	0.88[GIH][hapmap]
rs4711107	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4712980	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933583	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs733528	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348709	1.00[JPT][hapmap]
rs9348711	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9348712	1.00[JPT][hapmap]
rs9348716	1.00[JPT][hapmap]
rs9358932	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9358933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358934	1.00[JPT][hapmap]
rs9358935	1.00[JPT][hapmap]
rs9358937	1.00[JPT][hapmap]
rs9366652	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366653	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9379851	1.00[JPT][hapmap]
rs9379855	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9379856	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9379857	1.00[JPT][hapmap]
rs9379858	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9379859	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9379862	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9379864	1.00[JPT][hapmap]
rs9379870	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap]
rs9393705	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9393706	1.00[JPT][hapmap]
rs9393707	1.00[JPT][hapmap]
rs9393708	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9393709	0.90[GIH][hapmap]
rs9393710	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9393712	0.88[JPT][hapmap]
rs9393713	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9393714	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9467725	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4712981	BTN3A2	cis	lymphoblastoid	seeQTL
rs4712981	BTN3A2	cis	multi-tissue	Pritchard
rs4712981	BTN3A3	cis	cerebellum	SCAN
rs4712981	BTN3A3	cis	lymphoblastoid	seeQTL
rs4712981	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26352600-26364200	Weak transcription	NHEK	skin
2	chr6:26352800-26364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:26353000-26364200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:26355400-26364200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:26356200-26365400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:26356400-26364400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:26357400-26361600	Weak transcription	K562	blood
8	chr6:26359000-26364600	Enhancers	Fetal Thymus	thymus
9	chr6:26359800-26364200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:26360200-26364200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:26360600-26362000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:26360600-26364400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:26360800-26361600	Enhancers	Primary B cells from cord blood	blood
14	chr6:26360800-26361600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr6:26360800-26361600	Enhancers	HepG2	liver
16	chr6:26360800-26361800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:26360800-26362000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr6:26360800-26362000	Enhancers	Thymus	Thymus
19	chr6:26360800-26362200	Enhancers	Primary T cells from cord blood	blood
20	chr6:26360800-26362200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:26360800-26362200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:26360800-26364200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:26361000-26361600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr6:26361000-26361800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:26361000-26362000	Enhancers	Primary B cells from peripheral blood	blood
26	chr6:26361200-26362000	Enhancers	Duodenum Mucosa	Duodenum
27	chr6:26361200-26364200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:26361400-26361800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:26361400-26362000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:26361400-26362200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:26361400-26362200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr6:26361400-26362400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr6:26361400-26362400	Enhancers	GM12878-XiMat	blood
34	chr6:26361400-26362800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:26361400-26364200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:26361400-26364200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr6:26361400-26364200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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