Variant report

Variant	rs2496253
Chromosome Location	chr1:152081921-152081922
allele	C/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152008020..152010755-chr1:152080954..152084659,4	MCF-7	breast:
2	chr1:152007161..152009536-chr1:152080414..152082026,2	MCF-7	breast:
3	chr1:152054917..152058416-chr1:152081485..152084438,3	MCF-7	breast:
4	chr1:152042308..152047029-chr1:152081777..152083465,4	MCF-7	breast:
5	chr1:152019653..152021946-chr1:152081458..152082982,2	MCF-7	breast:
6	chr1:152064256..152066626-chr1:152081752..152084495,3	MCF-7	breast:
7	chr1:152023393..152025689-chr1:152081392..152083739,7	MCF-7	breast:
8	chr1:152039144..152040996-chr1:152081393..152082940,2	MCF-7	breast:
9	chr1:152081901..152084932-chr1:152421607..152423575,3	MCF-7	breast:
10	chr1:152018511..152020691-chr1:152081107..152083275,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10788821	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1131471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131473	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11588437	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs12033735	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1496036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1496041	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2069258	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2935208	1.00[CEU][hapmap];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]
rs2999563	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3001974	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3007680	0.82[JPT][hapmap]
rs3122305	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3124316	0.95[JPT][hapmap]
rs4579760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4845420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6700989	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs924087	0.85[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv438037	chr1:152079989-152084039	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2496253	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2496253	S100A10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152079800-152082000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
2	chr1:152079800-152082200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr1:152079800-152082800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:152079800-152083000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:152079800-152083200	ZNF genes & repeats	Lung	lung
6	chr1:152079800-152084400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:152079800-152085400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:152079800-152085400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
9	chr1:152080000-152082400	Flanking Bivalent TSS/Enh	HMEC	breast
10	chr1:152080000-152082600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
11	chr1:152080000-152082600	Bivalent/Poised TSS	NHLF	lung
12	chr1:152080000-152083800	ZNF genes & repeats	HSMM	muscle
13	chr1:152080000-152085000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
14	chr1:152080000-152085600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:152080200-152082000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr1:152080200-152082000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
17	chr1:152080200-152082200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
18	chr1:152080200-152082200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr1:152080400-152082800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr1:152080600-152082000	Bivalent Enhancer	Colonic Mucosa	Colon
21	chr1:152080800-152082000	Weak transcription	Gastric	stomach
22	chr1:152080800-152082800	Bivalent Enhancer	Liver	Liver
23	chr1:152080800-152084400	Flanking Bivalent TSS/Enh	Placenta	Placenta
24	chr1:152081000-152082800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr1:152081000-152083200	Bivalent Enhancer	Spleen	Spleen
26	chr1:152081000-152083200	Flanking Bivalent TSS/Enh	A549	lung
27	chr1:152081200-152082000	Bivalent Enhancer	HUVEC	blood vessel
28	chr1:152081400-152082000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:152081400-152082200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
30	chr1:152081400-152082400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:152081400-152082400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
32	chr1:152081400-152082600	Bivalent Enhancer	Fetal Intestine Large	intestine
33	chr1:152081400-152082800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
34	chr1:152081400-152083000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:152081400-152083000	Bivalent Enhancer	Fetal Thymus	thymus
36	chr1:152081400-152084400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
37	chr1:152081400-152085200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
38	chr1:152081400-152085400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:152081600-152082000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
40	chr1:152081600-152082000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
41	chr1:152081600-152082000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:152081600-152082000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr1:152081600-152082000	Bivalent Enhancer	NH-A	brain
44	chr1:152081600-152082200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:152081600-152082600	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
46	chr1:152081600-152083000	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr1:152081600-152083200	ZNF genes & repeats	HSMMtube	muscle
48	chr1:152081600-152083800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
49	chr1:152081600-152085200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:152081600-152085400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links