Variant report

Variant	rs17587597
Chromosome Location	chr6:25986451-25986452
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	POLR2A	chr6:25986333-25986769	GM12892	blood:	n/a	n/a
2	POLR2A	chr6:25986315-25986810	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:25981126-25993466	K562	blood:	n/a	n/a
4	POLR2A	chr6:25986431-25988643	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:25986339-25986813	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:25986260-25986820	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:25982445..25984066-chr6:25986097..25987824,2	MCF-7	breast:
2	chr6:25985799..25990027-chr6:25991112..25994943,7	MCF-7	breast:
3	chr6:25983493..25989204-chr6:25990743..25993962,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272065	TF binding region
ENSG00000272065	Chromatin interaction
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1045537	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10484433	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191445	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs13191776	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192365	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193424	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195279	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13195692	1.00[ASN][1000 genomes]
rs13196552	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197334	1.00[ASN][1000 genomes]
rs13198474	0.91[CEU][hapmap]
rs13199775	0.82[CEU][hapmap]
rs13200797	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs13200888	1.00[ASN][1000 genomes]
rs13200921	0.82[CEU][hapmap]
rs13201341	0.91[CEU][hapmap]
rs13201821	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13202371	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202688	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs13203673	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206443	1.00[ASN][1000 genomes]
rs13206501	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13207673	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13210399	1.00[ASN][1000 genomes]
rs13211947	0.91[CEU][hapmap]
rs13212534	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs13214169	0.84[EUR][1000 genomes]
rs13214280	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216785	1.00[ASN][1000 genomes]
rs13220395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220488	0.97[EUR][1000 genomes]
rs16891235	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891264	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891315	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs16891334	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs17526722	0.85[CEU][hapmap]
rs17528178	0.82[EUR][1000 genomes]
rs17586553	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17586784	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587226	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2051539	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298091	1.00[CHB][hapmap]
rs28360595	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34027471	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34116162	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34233736	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34391493	0.80[AMR][1000 genomes]
rs34525648	0.92[EUR][1000 genomes]
rs34791189	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34804024	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35069699	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35116528	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35169013	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35249036	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35335639	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35367169	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35378061	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35402046	1.00[ASN][1000 genomes]
rs35484309	1.00[ASN][1000 genomes]
rs35528636	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778245	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825164	1.00[ASN][1000 genomes]
rs35902160	1.00[ASN][1000 genomes]
rs36012762	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3734523	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3734528	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752417	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266779	0.82[EUR][1000 genomes]
rs56195001	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294283	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60512607	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66790453	1.00[ASN][1000 genomes]
rs67296946	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67491322	0.93[EUR][1000 genomes]
rs67844427	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68149500	1.00[ASN][1000 genomes]
rs68194335	0.80[EUR][1000 genomes]
rs6903228	0.92[EUR][1000 genomes]
rs6931120	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6939997	0.82[CEU][hapmap]
rs6940007	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6940698	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs71557312	0.82[EUR][1000 genomes]
rs71557315	0.83[ASN][1000 genomes]
rs71557316	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72832596	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72834617	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72834623	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748167	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[EUR][1000 genomes]
rs7749414	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750960	0.84[EUR][1000 genomes]
rs7766531	0.84[EUR][1000 genomes]
rs9295675	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461216	0.82[CEU][hapmap]
rs9461219	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs9461222	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[EUR][1000 genomes]
rs9461223	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467613	0.82[CEU][hapmap]
rs9467622	0.82[CEU][hapmap]
rs9467626	0.82[CEU][hapmap]
rs9467632	0.88[EUR][1000 genomes]
rs9467635	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs9467684	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	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
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17587597	BTN3A2	cis	lymphoblastoid	GTEx
rs17587597	HIST1H2BE	cis	lymphoblastoid	seeQTL
rs17587597	HIST1H2AC	cis	lymphoblastoid	seeQTL
rs17587597	BTN3A3	cis	lymphoblastoid	seeQTL
rs17587597	HIST1H2BD	cis	lymphoblastoid	seeQTL
rs17587597	BTN3A2	cis	lymphoblastoid	seeQTL
rs17587597	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs17587597	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25967200-25992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:25967800-25992000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:25968400-25987600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:25968600-25987200	Strong transcription	Duodenum Mucosa	Duodenum
5	chr6:25968800-25986600	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr6:25968800-25989400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:25969000-25986600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:25969000-25989600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:25969200-25989400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr6:25971400-25987200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:25971400-25989400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:25972200-25987800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:25972200-25988600	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:25972400-25986600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:25972400-25987200	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr6:25972400-25987400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:25972400-25988800	Strong transcription	HSMM	muscle
18	chr6:25972600-25986600	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr6:25972600-25988600	Strong transcription	Osteobl	bone
20	chr6:25972800-25992000	Weak transcription	Right Ventricle	heart
21	chr6:25973600-25987000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:25973600-25988000	Strong transcription	Placenta	Placenta
23	chr6:25973600-25989200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:25974600-25987600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:25974800-25992000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:25974800-25992000	Weak transcription	A549	lung
27	chr6:25975200-25987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:25975200-25988600	Strong transcription	Primary B cells from cord blood	blood
29	chr6:25976400-25992000	Weak transcription	NH-A	brain
30	chr6:25978600-25988800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:25979200-25988400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:25980200-25987000	Strong transcription	Fetal Thymus	thymus
33	chr6:25980200-25987200	Genic enhancers	Fetal Intestine Large	intestine
34	chr6:25980200-25988600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:25980200-25988800	Strong transcription	Adipose Nuclei	Adipose
36	chr6:25980400-25988600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:25980600-25986800	Strong transcription	Fetal Stomach	stomach
38	chr6:25980600-25987000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:25980600-25987200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:25980600-25988600	Strong transcription	Fetal Muscle Leg	muscle
41	chr6:25980600-25989400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:25980800-25986800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:25980800-25987000	Strong transcription	Primary T cells from cord blood	blood
44	chr6:25980800-25987200	Strong transcription	Spleen	Spleen
45	chr6:25981200-25988600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:25981200-25988600	Strong transcription	Thymus	Thymus
47	chr6:25981600-25987000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:25981600-25988600	Strong transcription	Lung	lung
49	chr6:25981600-25989400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:25982200-25989000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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