Variant report

Variant	rs17587226
Chromosome Location	chr6:25962304-25962305
allele	C/T
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	CTCF	chr6:25962240-25962390	GM06990	blood:	n/a	n/a
2	CTCF	chr6:25961991-25962745	K562	blood:	n/a	n/a
3	MTA3	chr6:25962288-25963326	GM12878	blood:	n/a	n/a
4	SPI1	chr6:25962293-25963534	GM12878	blood:	n/a	chr6:25962799-25962812
5	POLR2A	chr6:25962283-25964437	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:25962063-25963811	GM12892	blood:	n/a	n/a
7	POLR2A	chr6:25962270-25964265	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:25962118-25964847	GM12878	blood:	n/a	n/a
9	CTCF	chr6:25961989-25962340	GM12878	blood:	n/a	n/a
10	MAX	chr6:25962195-25963449	GM12878	blood:	n/a	chr6:25962830-25962839
11	MAFK	chr6:25962223-25963169	Hela-S3	cervix:	n/a	chr6:25962582-25962597
12	ZNF143	chr6:25961993-25963231	GM12878	blood:	n/a	chr6:25962903-25962912
13	RAD21	chr6:25961978-25962308	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:25961698-25964844	GM12891	blood:	n/a	n/a
15	RAD21	chr6:25961707-25962340	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF384	chr6:25962216-25963318	K562	blood:	n/a	n/a
17	CTCF	chr6:25962220-25962370	NHDF-neo	bronchial:	n/a	n/a
18	MAFK	chr6:25962110-25963338	K562	blood:	n/a	chr6:25962582-25962597
19	IRF1	chr6:25962100-25963450	K562	blood:	n/a	chr6:25962995-25963016 chr6:25962999-25963010 chr6:25962980-25962994 chr6:25962999-25963013 chr6:25963000-25963012 chr6:25963001-25963011 chr6:25962319-25962333
20	EBF1	chr6:25962145-25963412	GM12878	blood:	n/a	chr6:25962733-25962742 chr6:25962731-25962742 chr6:25962731-25962744 chr6:25962733-25962742 chr6:25962733-25962743
21	NFATC1	chr6:25962253-25963260	GM12878	blood:	n/a	n/a
22	TBL1XR1	chr6:25962188-25964158	K562	blood:	n/a	n/a
23	MTA3	chr6:25961955-25964175	GM12878	blood:	n/a	n/a
24	RAD21	chr6:25961993-25962346	HepG2	liver:	n/a	n/a
25	CTCF	chr6:25962220-25962370	RPTEC	kidney:	n/a	n/a
26	POLR2A	chr6:25962273-25963852	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25962020..25964518-chr6:25991024..25993046,2	MCF-7	breast:
2	chr6:25961783..25964529-chr6:25992813..25995946,4	MCF-7	breast:

Variant related genes	Relation type
TRIM38	TF binding region
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1045537	0.84[CEU][hapmap]
rs10484433	0.91[CEU][hapmap]
rs10484435	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13191445	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13191776	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13192365	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs13192713	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13193424	0.90[EUR][1000 genomes]
rs13195279	0.91[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13196552	0.91[CEU][hapmap]
rs13198474	0.91[CEU][hapmap]
rs13199775	0.82[CEU][hapmap]
rs13200797	0.88[CEU][hapmap]
rs13200921	0.82[CEU][hapmap]
rs13201341	0.91[CEU][hapmap]
rs13201821	0.91[CEU][hapmap]
rs13202371	0.90[EUR][1000 genomes]
rs13202592	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13202688	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13203673	0.93[EUR][1000 genomes]
rs13206501	0.84[CEU][hapmap]
rs13207673	0.91[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs13210041	0.81[EUR][1000 genomes]
rs13211947	0.91[CEU][hapmap]
rs13212534	0.89[CEU][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes]
rs13213957	0.91[CEU][hapmap]
rs13214280	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs13220395	1.00[CEU][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs13220488	0.90[EUR][1000 genomes]
rs16891235	0.91[CEU][hapmap]
rs16891261	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16891264	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16891315	0.84[CEU][hapmap]
rs16891334	0.84[CEU][hapmap]
rs17526722	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs17528178	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17586553	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17586784	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17587597	0.93[EUR][1000 genomes]
rs2051539	0.90[EUR][1000 genomes]
rs28360595	0.87[EUR][1000 genomes]
rs34027471	0.81[EUR][1000 genomes]
rs34116162	0.90[EUR][1000 genomes]
rs34233736	0.90[EUR][1000 genomes]
rs34525648	0.86[EUR][1000 genomes]
rs34804024	0.87[EUR][1000 genomes]
rs35069699	0.90[EUR][1000 genomes]
rs35169013	0.90[EUR][1000 genomes]
rs35378061	0.81[EUR][1000 genomes]
rs35506517	0.81[EUR][1000 genomes]
rs35528636	0.81[EUR][1000 genomes]
rs35778245	0.90[EUR][1000 genomes]
rs36012762	0.81[EUR][1000 genomes]
rs36014129	0.83[EUR][1000 genomes]
rs3734523	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes]
rs3734528	0.91[CEU][hapmap]
rs3752417	0.84[EUR][1000 genomes]
rs3884025	0.84[EUR][1000 genomes]
rs41266767	1.00[ASN][1000 genomes]
rs41266779	0.88[EUR][1000 genomes]
rs67491322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67844427	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6903228	0.86[EUR][1000 genomes]
rs6910549	1.00[GIH][hapmap]
rs6931120	0.86[EUR][1000 genomes]
rs6939997	0.82[CEU][hapmap]
rs6940007	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes]
rs6940698	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs71557312	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71557316	0.81[EUR][1000 genomes]
rs72832596	0.93[EUR][1000 genomes]
rs72834617	0.81[EUR][1000 genomes]
rs7748167	0.91[CEU][hapmap]
rs9295675	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs9461216	0.82[CEU][hapmap]
rs9461219	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs9461222	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs9461223	0.86[EUR][1000 genomes]
rs9467613	0.82[CEU][hapmap]
rs9467622	0.82[CEU][hapmap]
rs9467626	0.82[CEU][hapmap]
rs9467632	0.81[EUR][1000 genomes]
rs9467635	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs9467682	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17587226	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs17587226	BTN3A2	cis	lymphoblastoid	seeQTL
rs17587226	BTN3A3	cis	lymphoblastoid	seeQTL
rs17587226	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs17587226	BTN3A2	cis	lymphoblastoid	GTEx
rs17587226	BTN3A2	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25956000-25963000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25959600-25962400	Enhancers	Fetal Muscle Leg	muscle
3	chr6:25960600-25962400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:25960800-25962400	Weak transcription	Psoas Muscle	Psoas
5	chr6:25961600-25962400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr6:25961600-25962800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr6:25961600-25963000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:25961800-25962400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:25961800-25962400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:25961800-25962400	Enhancers	Fetal Muscle Trunk	muscle
11	chr6:25961800-25962400	Enhancers	Right Atrium	heart
12	chr6:25961800-25962400	Enhancers	HUVEC	blood vessel
13	chr6:25961800-25962600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:25961800-25962600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:25961800-25962600	Flanking Active TSS	Colon Smooth Muscle	Colon
16	chr6:25961800-25962600	Enhancers	Lung	lung
17	chr6:25961800-25962800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr6:25961800-25962800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr6:25961800-25962800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr6:25961800-25962800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr6:25961800-25962800	Enhancers	Small Intestine	intestine
22	chr6:25961800-25962800	Enhancers	Spleen	Spleen
23	chr6:25961800-25962800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr6:25961800-25963000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr6:25961800-25963000	Flanking Active TSS	Dnd41	blood
26	chr6:25962000-25962400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:25962000-25962400	Weak transcription	Aorta	Aorta
28	chr6:25962000-25962400	Enhancers	Liver	Liver
29	chr6:25962000-25962400	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:25962000-25962400	Enhancers	Esophagus	oesophagus
31	chr6:25962000-25962400	Enhancers	Fetal Intestine Large	intestine
32	chr6:25962000-25962400	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr6:25962000-25962400	Enhancers	Thymus	Thymus
34	chr6:25962000-25962400	Flanking Active TSS	HepG2	liver
35	chr6:25962000-25962400	Enhancers	HMEC	breast
36	chr6:25962000-25962400	Enhancers	NHEK	skin
37	chr6:25962000-25962400	Enhancers	NHLF	lung
38	chr6:25962000-25962600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:25962000-25962600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:25962000-25962600	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr6:25962000-25962600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr6:25962000-25962600	Enhancers	Placenta	Placenta
43	chr6:25962000-25962600	Enhancers	Pancreas	Pancrea
44	chr6:25962000-25962600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:25962000-25962600	Flanking Active TSS	HSMM	muscle
46	chr6:25962000-25962800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:25962000-25962800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr6:25962000-25962800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:25962000-25962800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:25962000-25962800	Flanking Active TSS	Hela-S3	cervix

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