Variant report

Variant	rs56223691
Chromosome Location	chr1:174135887-174135888
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174126360..174131591-chr1:174135566..174140144,7	MCF-7	breast:
2	chr1:174134604..174137057-chr1:174160693..174163339,2	K562	blood:
3	chr1:174128029..174130536-chr1:174135195..174136923,2	MCF-7	breast:
4	chr1:174134604..174137311-chr1:174161839..174164526,2	K562	blood:
5	chr1:173999328..174000926-chr1:174134327..174136474,2	K562	blood:
6	chr1:174134591..174137742-chr1:174149123..174151486,3	K562	blood:

Variant related genes	Relation type
ENSG00000152061	Chromatin interaction
ENSG00000227373	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs55687343	0.87[AFR][1000 genomes]
rs55773127	1.00[AFR][1000 genomes]
rs56106938	0.93[AFR][1000 genomes]
rs56179605	0.87[AFR][1000 genomes]
rs56204297	1.00[AFR][1000 genomes]
rs56713956	0.93[AFR][1000 genomes]
rs57774157	0.93[AFR][1000 genomes]
rs58997380	0.87[AFR][1000 genomes]
rs59753012	0.87[AFR][1000 genomes]
rs60717080	0.93[AFR][1000 genomes]
rs60843796	0.87[AFR][1000 genomes]
rs61077309	1.00[AFR][1000 genomes]
rs61288130	1.00[AFR][1000 genomes]
rs74128305	0.87[AFR][1000 genomes]
rs74128306	0.87[AFR][1000 genomes]
rs74128315	0.85[AFR][1000 genomes]
rs74128317	0.93[AFR][1000 genomes]
rs74128318	0.93[AFR][1000 genomes]
rs74128319	0.93[AFR][1000 genomes]
rs74128320	1.00[AFR][1000 genomes]
rs74128321	1.00[AFR][1000 genomes]
rs74128322	0.93[AFR][1000 genomes]
rs74128323	0.93[AFR][1000 genomes]
rs74128324	0.93[AFR][1000 genomes]
rs74128326	0.93[AFR][1000 genomes]
rs74128329	0.93[AFR][1000 genomes]
rs74128334	0.87[AFR][1000 genomes]
rs74128342	0.87[AFR][1000 genomes]
rs74128343	0.87[AFR][1000 genomes]
rs74128344	1.00[AFR][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	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong 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	15 gene(s)	inside rSNPs	diseases
9	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174129600-174164800	Weak transcription	Gastric	stomach
2	chr1:174129600-174173200	Weak transcription	Pancreas	Pancrea
3	chr1:174129800-174137000	Weak transcription	Fetal Lung	lung
4	chr1:174129800-174145600	Weak transcription	Fetal Thymus	thymus
5	chr1:174129800-174147000	Weak transcription	Fetal Brain Male	brain
6	chr1:174129800-174149600	Weak transcription	Aorta	Aorta
7	chr1:174130000-174136200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:174130000-174144400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:174130000-174157600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:174130200-174138000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:174130200-174143200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:174130200-174145000	Weak transcription	NHEK	skin
13	chr1:174130200-174145600	Weak transcription	Fetal Stomach	stomach
14	chr1:174130200-174147400	Weak transcription	Hela-S3	cervix
15	chr1:174130800-174138200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:174130800-174156600	Weak transcription	Primary T cells from cord blood	blood
17	chr1:174131200-174138800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:174131400-174136600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:174132600-174136000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:174132600-174136600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:174132600-174138400	Weak transcription	Right Atrium	heart
22	chr1:174133000-174140600	Enhancers	Fetal Heart	heart
23	chr1:174134000-174136800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:174134000-174139600	Enhancers	Primary B cells from peripheral blood	blood
25	chr1:174134200-174143600	Weak transcription	Fetal Intestine Large	intestine
26	chr1:174134600-174136600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:174134800-174136000	Enhancers	Brain Hippocampus Middle	brain
28	chr1:174134800-174136200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:174134800-174136400	Enhancers	Liver	Liver
30	chr1:174134800-174137200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr1:174134800-174159800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:174135000-174136000	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:174135000-174136400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:174135000-174136800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:174135000-174136800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr1:174135000-174138400	Weak transcription	Left Ventricle	heart
37	chr1:174135200-174136000	Enhancers	Brain Anterior Caudate	brain
38	chr1:174135200-174136400	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr1:174135200-174137000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:174135200-174138600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:174135200-174139000	Weak transcription	HepG2	liver
42	chr1:174135200-174143200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:174135400-174136000	Enhancers	Fetal Intestine Small	intestine
44	chr1:174135400-174136200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:174135400-174136200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr1:174135400-174136400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:174135400-174136400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr1:174135400-174136800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr1:174135600-174136000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:174135600-174136000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links