Variant report

Variant	rs17140098
Chromosome Location	chr6:5288320-5288321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5284244..5290564-chr6:5292142..5296092,7	K562	blood:
2	chr6:5287945..5289983-chr6:5297023..5298876,2	K562	blood:
3	chr6:5259520..5261609-chr6:5287252..5289754,2	K562	blood:
4	chr6:5285992..5290262-chr6:5291687..5294091,5	K562	blood:
5	chr6:5260357..5262137-chr6:5285896..5288338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214113	Chromatin interaction
ENSG00000145982	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17140091	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17140145	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34382405	1.00[AMR][1000 genomes]
rs4516991	1.00[AMR][1000 genomes]
rs4516992	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv1016456	chr6:5216835-5315913	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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
16	nsv538117	chr6:5216835-5315913	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	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
18	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
19	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
20	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
21	nsv1022911	chr6:5286297-5322133	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv538119	chr6:5286297-5322133	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5262400-5302400	Weak transcription	Aorta	Aorta
2	chr6:5263000-5301000	Weak transcription	Fetal Brain Male	brain
3	chr6:5263800-5291800	Weak transcription	Fetal Intestine Small	intestine
4	chr6:5267000-5290400	Weak transcription	HepG2	liver
5	chr6:5268000-5294400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:5275000-5290400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:5276600-5294000	Weak transcription	Fetal Intestine Large	intestine
8	chr6:5279200-5289800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:5279400-5298200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:5280400-5294000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:5280600-5289800	Weak transcription	Primary B cells from cord blood	blood
12	chr6:5280800-5289400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:5280800-5293200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:5280800-5308200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:5281000-5294400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:5281400-5293400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:5282600-5292200	Weak transcription	Fetal Heart	heart
18	chr6:5285400-5294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:5286000-5288600	Enhancers	GM12878-XiMat	blood
20	chr6:5286200-5294000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:5287000-5288600	Enhancers	NHLF	lung
22	chr6:5287200-5288400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:5287200-5288400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:5287200-5288400	Enhancers	Esophagus	oesophagus
25	chr6:5287200-5288400	Enhancers	Left Ventricle	heart
26	chr6:5287200-5288400	Enhancers	Right Atrium	heart
27	chr6:5287200-5288400	Enhancers	Spleen	Spleen
28	chr6:5287200-5288600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:5287200-5288600	Enhancers	HMEC	breast
30	chr6:5287200-5288600	Enhancers	NHDF-Ad	bronchial
31	chr6:5287200-5288800	Enhancers	Right Ventricle	heart
32	chr6:5287200-5289000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr6:5287200-5289000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:5287400-5288400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:5287400-5288400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:5287400-5288400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:5287400-5288400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:5287400-5288400	Enhancers	Brain Hippocampus Middle	brain
39	chr6:5287400-5288400	Enhancers	Fetal Muscle Leg	muscle
40	chr6:5287400-5288400	Enhancers	Pancreas	Pancrea
41	chr6:5287400-5288400	Enhancers	K562	blood
42	chr6:5287400-5288600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:5287400-5288600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:5287400-5288600	Enhancers	Adipose Nuclei	Adipose
45	chr6:5287400-5288600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr6:5287400-5288600	Enhancers	Stomach Mucosa	stomach
47	chr6:5287400-5288800	Enhancers	Psoas Muscle	Psoas
48	chr6:5287400-5288800	Enhancers	HSMM	muscle
49	chr6:5287400-5296200	Weak transcription	Thymus	Thymus
50	chr6:5287600-5288400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links