Variant report

Variant	rs1776008
Chromosome Location	chr9:5818970-5818971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5816326..5818970-chr9:6006869..6008999,2	MCF-7	breast:
2	chr9:5816098..5820719-chr9:5821710..5826466,5	MCF-7	breast:
3	chr9:5818554..5820772-chr9:5831494..5833266,2	MCF-7	breast:
4	chr9:5812841..5814802-chr9:5818436..5820936,2	K562	blood:

Variant related genes	Relation type
ENSG00000183354	Chromatin interaction
ENSG00000099219	Chromatin interaction
ENSG00000263575	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10733517	1.00[TSI][hapmap]
rs10758734	1.00[TSI][hapmap]
rs10815335	1.00[TSI][hapmap]
rs10975340	1.00[EUR][1000 genomes]
rs1141025	1.00[EUR][1000 genomes]
rs12339889	1.00[MEX][hapmap]
rs12342282	1.00[MEX][hapmap]
rs1260128	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1260130	0.89[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260132	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1260134	0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1260135	1.00[EUR][1000 genomes]
rs16923356	1.00[MEX][hapmap]
rs16923371	1.00[MEX][hapmap]
rs1745887	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1745888	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1993912	1.00[MEX][hapmap]
rs2150703	1.00[TSI][hapmap]
rs2476262	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760408	1.00[EUR][1000 genomes]
rs2760409	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760410	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2797512	0.89[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2797514	1.00[EUR][1000 genomes]
rs2797516	0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2797517	0.88[AFR][1000 genomes]
rs2797519	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs343500	1.00[TSI][hapmap]
rs3739649	1.00[TSI][hapmap]
rs4395943	1.00[TSI][hapmap]
rs4742131	1.00[TSI][hapmap]
rs58370080	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6477001	1.00[EUR][1000 genomes]
rs6477002	1.00[EUR][1000 genomes]
rs7024130	1.00[TSI][hapmap]
rs7034210	1.00[TSI][hapmap]
rs7037680	0.88[ASW][hapmap];0.97[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7038243	1.00[YRI][hapmap]
rs7042100	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7042539	0.84[AFR][1000 genomes]
rs7046793	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73377834	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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 target site	31 gene(s)	inside rSNPs	diseases
3	nsv892151	chr9:5602528-5841438	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5779200-5832200	Weak transcription	Fetal Brain Male	brain
2	chr9:5779600-5827800	Weak transcription	Small Intestine	intestine
3	chr9:5784200-5831600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:5786800-5832200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:5787000-5830200	Weak transcription	Dnd41	blood
6	chr9:5787400-5832000	Weak transcription	Fetal Brain Female	brain
7	chr9:5787600-5831600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:5787600-5832000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:5787600-5832200	Weak transcription	Esophagus	oesophagus
10	chr9:5789800-5825200	Weak transcription	Gastric	stomach
11	chr9:5790000-5824000	Weak transcription	Pancreas	Pancrea
12	chr9:5794600-5821800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:5794600-5825600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:5797400-5831400	Weak transcription	Psoas Muscle	Psoas
15	chr9:5798400-5831200	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:5799800-5824000	Weak transcription	Aorta	Aorta
17	chr9:5799800-5825200	Weak transcription	Brain Angular Gyrus	brain
18	chr9:5799800-5825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:5799800-5831600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:5799800-5831800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:5799800-5831800	Weak transcription	HUVEC	blood vessel
22	chr9:5800400-5826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr9:5801200-5823800	Weak transcription	Fetal Heart	heart
24	chr9:5801200-5824800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:5801800-5823000	Weak transcription	Fetal Intestine Small	intestine
26	chr9:5802000-5820800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:5802000-5824200	Weak transcription	Thymus	Thymus
28	chr9:5802000-5828200	Weak transcription	Stomach Mucosa	stomach
29	chr9:5802200-5825200	Weak transcription	Fetal Lung	lung
30	chr9:5802200-5831200	Weak transcription	Colonic Mucosa	Colon
31	chr9:5802200-5831600	Weak transcription	Fetal Kidney	kidney
32	chr9:5802800-5831400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:5806800-5823000	Weak transcription	Fetal Stomach	stomach
34	chr9:5809000-5823800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr9:5809200-5823200	Weak transcription	Spleen	Spleen
36	chr9:5810200-5820400	Weak transcription	Brain Substantia Nigra	brain
37	chr9:5810200-5831800	Weak transcription	Brain Germinal Matrix	brain
38	chr9:5810400-5820600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:5810400-5820600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:5810400-5822600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr9:5810400-5823800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:5810800-5820600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr9:5810800-5822600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:5810800-5825600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:5810800-5829600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr9:5811600-5823000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:5812000-5832200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr9:5812200-5824000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:5812600-5824200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:5812800-5821200	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links