Variant report

Variant	rs2753253
Chromosome Location	chr6:5322762-5322763
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5316201..5319010-chr6:5321352..5323470,3	K562	blood:
2	chr6:5316219..5318124-chr6:5321436..5323216,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2552300	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2552301	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753254	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];0.98[ASN][1000 genomes]
rs3763182	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs55716067	0.90[ASN][1000 genomes]
rs62386863	0.90[ASN][1000 genomes]
rs62386900	0.82[ASN][1000 genomes]
rs708036	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72815645	0.85[ASN][1000 genomes]
rs7774214	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs797128	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs797131	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs797136	0.81[YRI][hapmap]
rs809962	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378421	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9378422	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs9378946	0.82[ASN][1000 genomes]
rs9392079	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs9392676	0.82[ASN][1000 genomes]
rs9392678	0.81[ASN][1000 genomes]
rs9405818	0.81[JPT][hapmap]
rs9405819	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9405820	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9405821	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9405824	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9405826	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9405828	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs9405829	0.85[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1022738	chr6:5298362-5411645	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv600883	chr6:5302619-5400658	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv883417	chr6:5307432-5431340	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv1015643	chr6:5311590-5452427	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv883419	chr6:5316399-5400658	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5288400-5324000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:5288400-5331000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:5292800-5334400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:5295400-5325000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:5303200-5368800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:5303600-5332400	Weak transcription	Gastric	stomach
7	chr6:5304000-5325400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:5304000-5326000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr6:5304000-5337600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:5304200-5322800	Weak transcription	Pancreas	Pancrea
11	chr6:5307000-5323800	Weak transcription	HepG2	liver
12	chr6:5308800-5325000	Weak transcription	Primary T cells from cord blood	blood
13	chr6:5308800-5325000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:5309200-5333400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:5309200-5334000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:5313800-5322800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:5314800-5323800	Weak transcription	GM12878-XiMat	blood
18	chr6:5315000-5326400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:5316400-5323800	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:5316400-5324200	Weak transcription	Lung	lung
21	chr6:5316400-5333800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:5316800-5335200	Weak transcription	NHLF	lung
23	chr6:5317200-5325000	Weak transcription	Left Ventricle	heart
24	chr6:5317400-5323600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:5317400-5323800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:5317600-5324000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:5318200-5323600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:5318200-5324400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:5318800-5331600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:5319200-5328200	Weak transcription	Thymus	Thymus
31	chr6:5319600-5323800	Weak transcription	Psoas Muscle	Psoas
32	chr6:5319600-5334600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:5320400-5323000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:5320600-5344400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:5321000-5325400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:5321400-5322800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:5321400-5323200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:5321400-5327600	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:5321600-5323200	Enhancers	Fetal Intestine Large	intestine
40	chr6:5321600-5323200	Enhancers	Fetal Intestine Small	intestine
41	chr6:5321800-5335200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr6:5322200-5333800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:5322400-5323000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr6:5322600-5333600	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links