Variant report

Variant	rs773423
Chromosome Location	chr7:40017848-40017849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39988014..39992779-chr7:40016991..40021232,5	K562	blood:
2	chr7:39986728..39990828-chr7:40016183..40019996,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259826	Chromatin interaction
ENSG00000065883	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1082021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1082022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1082024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1082026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1082027	1.00[AMR][1000 genomes]
rs1082033	1.00[AMR][1000 genomes]
rs12113257	1.00[AMR][1000 genomes]
rs1257697	1.00[AMR][1000 genomes]
rs1257711	1.00[AMR][1000 genomes]
rs1314087	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1829909	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55825872	1.00[AMR][1000 genomes]
rs55913371	1.00[AMR][1000 genomes]
rs56684313	1.00[AMR][1000 genomes]
rs58681548	1.00[AMR][1000 genomes]
rs73687511	1.00[AMR][1000 genomes]
rs73687519	1.00[AMR][1000 genomes]
rs773380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773389	1.00[YRI][hapmap]
rs773394	1.00[AMR][1000 genomes]
rs773396	1.00[AMR][1000 genomes]
rs773400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773401	1.00[AMR][1000 genomes]
rs773404	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773406	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773408	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs773409	1.00[YRI][hapmap]
rs773416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773418	1.00[AMR][1000 genomes]
rs773419	1.00[AMR][1000 genomes]
rs773420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773421	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs773422	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs808913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9942572	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:39994200-40027200	Weak transcription	HSMM	muscle
3	chr7:39994800-40018000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:39995000-40018200	Weak transcription	Spleen	Spleen
5	chr7:39995200-40042600	Weak transcription	K562	blood
6	chr7:39997800-40027400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:39998000-40027200	Weak transcription	Hela-S3	cervix
8	chr7:40001000-40018600	Weak transcription	Thymus	Thymus
9	chr7:40001200-40018200	Weak transcription	Fetal Thymus	thymus
10	chr7:40005600-40021000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr7:40005600-40021000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr7:40006600-40018200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr7:40006600-40019800	Enhancers	Primary B cells from peripheral blood	blood
14	chr7:40006800-40031200	Weak transcription	Fetal Stomach	stomach
15	chr7:40007200-40027200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:40007600-40027200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:40008800-40018200	Weak transcription	Right Atrium	heart
18	chr7:40009400-40020800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr7:40009400-40027200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr7:40009400-40027400	Weak transcription	Osteobl	bone
21	chr7:40009600-40018000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:40009600-40027400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:40009800-40027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:40010000-40024600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:40010000-40026800	Weak transcription	NHEK	skin
26	chr7:40010200-40025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:40010400-40027200	Weak transcription	Esophagus	oesophagus
28	chr7:40011000-40021000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr7:40011200-40023600	Weak transcription	Lung	lung
30	chr7:40011200-40025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:40011400-40027400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr7:40012200-40018000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:40014200-40021200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr7:40014800-40018600	Enhancers	Right Ventricle	heart
35	chr7:40014800-40021200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr7:40015000-40023600	Weak transcription	Fetal Intestine Small	intestine
37	chr7:40015400-40018200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:40015800-40018200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr7:40015800-40019200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr7:40015800-40019200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:40016000-40018200	Weak transcription	Left Ventricle	heart
42	chr7:40016000-40019000	Weak transcription	Pancreas	Pancrea
43	chr7:40016000-40021000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:40016200-40020200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:40016400-40019600	Enhancers	Primary T cells fromperipheralblood	blood
46	chr7:40016400-40020200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:40016600-40018600	Enhancers	Rectal Smooth Muscle	rectum
48	chr7:40016600-40019400	Enhancers	Brain Substantia Nigra	brain
49	chr7:40016600-40019400	Enhancers	Dnd41	blood
50	chr7:40016600-40019600	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links