Variant report

Variant	rs6465652
Chromosome Location	chr7:97739777-97739778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97650628..97651440-chr7:97739722..97740636,2	MCF-7	breast:
2	chr7:97738785..97741480-chr7:97751864..97754009,2	MCF-7	breast:
3	chr7:97733859..97737866-chr7:97738343..97741740,8	K562	blood:
4	chr7:97737823..97740365-chr7:97743059..97746026,2	K562	blood:
5	chr7:97739559..97743131-chr7:97746340..97751154,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164715	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10280984	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12704968	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1464739	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1880303	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1969007	1.00[EUR][1000 genomes]
rs1983439	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2088171	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2172885	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4318996	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs4509254	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4727387	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6465656	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6465659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6943900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6943971	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6945999	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6948785	1.00[YRI][hapmap]
rs6956383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6970100	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6971967	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6975661	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73406084	1.00[AMR][1000 genomes]
rs73709070	1.00[EUR][1000 genomes]
rs7788829	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792787	1.00[EUR][1000 genomes]
rs7800032	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7805804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs847561	1.00[EUR][1000 genomes]
rs865337	1.00[EUR][1000 genomes]
rs903593	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs982466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97737000-97745200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:97737000-97746200	Weak transcription	Spleen	Spleen
3	chr7:97737200-97741800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:97737200-97741800	Weak transcription	Lung	lung
5	chr7:97737200-97745600	Weak transcription	Gastric	stomach
6	chr7:97737200-97746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:97737200-97762400	Weak transcription	Aorta	Aorta
8	chr7:97737200-97764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:97737400-97741800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr7:97737400-97743400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:97737400-97744400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:97737600-97739800	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr7:97737600-97740800	Weak transcription	Pancreas	Pancrea
14	chr7:97737600-97741400	Enhancers	Fetal Intestine Large	intestine
15	chr7:97737600-97741600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:97737600-97754400	Weak transcription	HSMMtube	muscle
17	chr7:97737600-97762400	Weak transcription	Small Intestine	intestine
18	chr7:97737800-97739800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr7:97737800-97740400	Weak transcription	Psoas Muscle	Psoas
20	chr7:97737800-97741000	Enhancers	Fetal Intestine Small	intestine
21	chr7:97737800-97741200	Enhancers	Fetal Brain Male	brain
22	chr7:97737800-97743600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr7:97737800-97745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:97737800-97748600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:97737800-97749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:97737800-97751000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:97737800-97759600	Weak transcription	Right Ventricle	heart
28	chr7:97737800-97760800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:97737800-97767000	Weak transcription	Fetal Stomach	stomach
30	chr7:97738000-97739800	Weak transcription	Right Atrium	heart
31	chr7:97738000-97740600	Weak transcription	Stomach Mucosa	stomach
32	chr7:97738000-97743000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:97738000-97746200	Weak transcription	NHEK	skin
34	chr7:97738000-97748400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:97738000-97748400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:97738000-97751600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr7:97738200-97739800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr7:97738200-97740000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr7:97738200-97740000	Weak transcription	NHDF-Ad	bronchial
40	chr7:97738400-97742800	Weak transcription	Primary B cells from cord blood	blood
41	chr7:97738600-97740000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr7:97738600-97740200	Enhancers	Liver	Liver
43	chr7:97738600-97740400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr7:97738600-97741400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:97738600-97741400	Weak transcription	Primary T cells from cord blood	blood
46	chr7:97738600-97742800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:97738600-97744400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr7:97738800-97740400	Enhancers	H1 Cell Line	embryonic stem cell
49	chr7:97738800-97759200	Weak transcription	Dnd41	blood
50	chr7:97739000-97739800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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