Variant report

Variant	rs2295497
Chromosome Location	chr4:2877658-2877659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2876022..2879054-chr4:2934409..2936795,3	MCF-7	breast:
2	chr4:2876464..2878755-chr4:2882679..2884281,2	K562	blood:

Variant related genes	Relation type
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10010434	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13106867	1.00[LWK][hapmap]
rs231712	1.00[CEU][hapmap]
rs2846033	0.89[ASN][1000 genomes]
rs2858039	1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs3213502	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4690006	1.00[YRI][hapmap]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2295497	RND3	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2870600-2886000	Weak transcription	Fetal Brain Male	brain
3	chr4:2870800-2877800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:2870800-2878800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:2871000-2885800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:2871200-2881600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:2871200-2886000	Weak transcription	Aorta	Aorta
8	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:2871400-2879400	Weak transcription	Gastric	stomach
11	chr4:2871600-2880800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:2871800-2877800	Weak transcription	Fetal Brain Female	brain
13	chr4:2871800-2880400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:2872200-2890800	Weak transcription	A549	lung
15	chr4:2872600-2877800	Enhancers	Brain Hippocampus Middle	brain
16	chr4:2873600-2878000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:2874000-2883600	Weak transcription	NH-A	brain
18	chr4:2874000-2887000	Weak transcription	Fetal Heart	heart
19	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
20	chr4:2874400-2880200	Weak transcription	HSMMtube	muscle
21	chr4:2874600-2878000	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:2875000-2878800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:2875000-2879600	Weak transcription	Psoas Muscle	Psoas
24	chr4:2875000-2879800	Weak transcription	Spleen	Spleen
25	chr4:2875000-2880600	Weak transcription	Esophagus	oesophagus
26	chr4:2875400-2879600	Weak transcription	HUVEC	blood vessel
27	chr4:2875400-2880600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:2875400-2886000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr4:2875800-2878800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:2875800-2884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:2876000-2881800	Strong transcription	Fetal Intestine Small	intestine
32	chr4:2876000-2884000	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:2876000-2885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:2876000-2886000	Weak transcription	Colonic Mucosa	Colon
35	chr4:2876000-2886600	Weak transcription	Stomach Mucosa	stomach
36	chr4:2876400-2877800	Enhancers	Right Atrium	heart
37	chr4:2876400-2891600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:2876600-2877800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:2876600-2882600	Strong transcription	Fetal Stomach	stomach
40	chr4:2876600-2889600	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:2876800-2877800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr4:2876800-2878000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:2876800-2881800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:2876800-2889000	Strong transcription	GM12878-XiMat	blood
46	chr4:2876800-2889400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr4:2876800-2891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:2877000-2877800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:2877000-2877800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:2877000-2878200	Strong transcription	HSMM	muscle

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