Variant report

Variant	rs6680324
Chromosome Location	chr1:209921193-209921194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:209865847..209866908-chr1:209920647..209921937,5	K562	blood:
2	chr1:209763958..209764607-chr1:209920721..209921610,2	MCF-7	breast:
3	chr1:209775290..209776004-chr1:209920694..209921561,3	K562	blood:
4	chr1:209917192..209919277-chr1:209920875..209922464,2	K562	blood:
5	chr1:209819912..209820560-chr1:209920680..209921530,2	MCF-7	breast:
6	chr1:209865971..209866599-chr1:209921080..209921833,2	MCF-7	breast:
7	chr1:209749839..209750375-chr1:209920675..209921983,3	MCF-7	breast:
8	chr1:209898273..209898882-chr1:209921133..209921700,3	MCF-7	breast:
9	chr1:209750094..209750827-chr1:209920765..209921786,7	K562	blood:
10	chr1:209739402..209740077-chr1:209920611..209921381,2	K562	blood:
11	chr1:209775181..209776051-chr1:209920704..209921451,3	MCF-7	breast:
12	chr1:209742327..209743226-chr1:209920951..209921587,3	MCF-7	breast:
13	chr1:209920122..209922907-chr1:209973621..209976183,2	MCF-7	breast:
14	chr1:209742263..209743556-chr1:209920676..209921449,8	K562	blood:
15	chr1:209920917..209921835-chr1:210162910..210163551,2	K562	blood:
16	chr1:209913450..209916086-chr1:209919671..209921571,2	K562	blood:
17	chr1:209800921..209801627-chr1:209920949..209921660,2	MCF-7	breast:
18	chr1:209921083..209924525-chr1:209927225..209931869,7	K562	blood:
19	chr1:209916474..209918920-chr1:209920104..209922211,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000009790	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000236136	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10489341	0.81[ASW][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11119333	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11799643	0.87[ASW][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs12024779	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12040780	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075595	1.00[EUR][1000 genomes]
rs17015053	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015095	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];1.00[ASN][1000 genomes]
rs17015099	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56679555	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57606822	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57756261	0.90[AFR][1000 genomes]
rs58627173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60132042	0.93[ASN][1000 genomes]
rs61279558	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089418	0.93[ASN][1000 genomes]
rs7532021	0.85[AFR][1000 genomes]
rs846909	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs846911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs846914	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs860185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs861762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209919600-209922400	Enhancers	Fetal Heart	heart
2	chr1:209919800-209923400	Enhancers	Fetal Intestine Small	intestine
3	chr1:209920400-209921600	Enhancers	Gastric	stomach
4	chr1:209920400-209921800	Enhancers	HMEC	breast
5	chr1:209920600-209921800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:209920800-209921200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:209920800-209921200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:209920800-209921200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:209920800-209921200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:209920800-209921200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:209920800-209921200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr1:209920800-209921200	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:209920800-209921200	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr1:209920800-209921200	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr1:209920800-209921200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr1:209920800-209921200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:209920800-209921200	Flanking Active TSS	Stomach Mucosa	stomach
18	chr1:209920800-209921200	Flanking Active TSS	NHEK	skin
19	chr1:209920800-209921400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:209920800-209921400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:209920800-209921400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:209920800-209921400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:209920800-209921400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr1:209920800-209921400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr1:209920800-209921400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:209920800-209921400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr1:209920800-209921400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr1:209920800-209921400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
29	chr1:209920800-209921400	Enhancers	Hela-S3	cervix
30	chr1:209920800-209921400	Active TSS	HSMM	muscle
31	chr1:209920800-209921400	Flanking Active TSS	NH-A	brain
32	chr1:209920800-209921600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:209920800-209921600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr1:209920800-209921600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr1:209920800-209921600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:209920800-209921600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:209920800-209921600	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:209920800-209921600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:209920800-209921600	Enhancers	HUVEC	blood vessel
40	chr1:209920800-209921600	Flanking Active TSS	K562	blood
41	chr1:209920800-209921600	Enhancers	NHLF	lung
42	chr1:209920800-209921800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:209920800-209921800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:209920800-209921800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:209920800-209921800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:209920800-209921800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr1:209920800-209921800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:209920800-209921800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr1:209920800-209921800	Enhancers	Liver	Liver
50	chr1:209920800-209921800	Active TSS	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links