Variant report

Variant	rs4235404
Chromosome Location	chr4:103440065-103440066
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103439093..103441146-chr4:103445747..103447716,2	MCF-7	breast:
2	chr4:103421285..103424744-chr4:103439488..103445746,9	MCF-7	breast:
3	chr4:103438272..103440503-chr4:103440992..103443713,2	MCF-7	breast:
4	chr4:103421746..103424260-chr4:103437368..103440522,4	K562	blood:
5	chr4:103438442..103440658-chr4:103444124..103446101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.80[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	0.83[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs118882	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12509517	0.80[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1585213	1.00[JPT][hapmap]
rs1585215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1599961	1.00[JPT][hapmap]
rs17032683	1.00[YRI][hapmap]
rs17032705	1.00[JPT][hapmap]
rs170731	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1801	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230492	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230500	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230504	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230505	1.00[JPT][hapmap]
rs230509	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230511	1.00[CEU][hapmap]
rs230514	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230515	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs230516	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs230519	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230520	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230526	1.00[JPT][hapmap]
rs230528	1.00[JPT][hapmap]
rs230529	1.00[JPT][hapmap]
rs230531	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230532	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230533	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230534	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230535	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs230539	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230540	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230541	0.91[JPT][hapmap]
rs230542	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2903281	1.00[YRI][hapmap]
rs3755867	0.91[JPT][hapmap]
rs3774933	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs3774936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap]
rs3774963	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs3774964	0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.91[JPT][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	1.00[JPT][hapmap]
rs4648055	0.87[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4648058	0.91[JPT][hapmap]
rs4648068	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	0.87[CEU][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4698861	0.82[CEU][hapmap]
rs4699030	0.91[JPT][hapmap]
rs747559	1.00[JPT][hapmap]
rs9790601	0.91[JPT][hapmap]
rs980455	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats 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
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4235404	RGS20	trans	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103423800-103445800	Weak transcription	Lung	lung
2	chr4:103424000-103446000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:103424800-103442400	Weak transcription	HSMM	muscle
4	chr4:103425200-103456400	Weak transcription	Osteobl	bone
5	chr4:103425600-103448400	Weak transcription	Fetal Thymus	thymus
6	chr4:103426000-103444400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:103426000-103452600	Weak transcription	NH-A	brain
8	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
9	chr4:103426200-103445800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:103426400-103442800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:103426400-103442800	Weak transcription	NHEK	skin
12	chr4:103426400-103450000	Weak transcription	HMEC	breast
13	chr4:103426400-103452600	Weak transcription	HSMMtube	muscle
14	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:103428000-103442600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:103428000-103449200	Weak transcription	Fetal Kidney	kidney
17	chr4:103429200-103446200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:103431800-103447000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
20	chr4:103434000-103442800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:103434000-103446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:103435000-103440800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr4:103436000-103441000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:103436000-103448600	Weak transcription	HUVEC	blood vessel
25	chr4:103438000-103444200	Weak transcription	Fetal Lung	lung
26	chr4:103438000-103448200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr4:103438200-103445200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:103438200-103445400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr4:103438200-103448200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:103438400-103440800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:103438400-103446800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:103438600-103445600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr4:103438600-103446000	Weak transcription	Fetal Intestine Large	intestine
34	chr4:103438800-103440200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:103438800-103441200	Enhancers	Primary T cells from cord blood	blood
36	chr4:103439000-103440200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:103439000-103440200	Enhancers	Small Intestine	intestine
38	chr4:103439000-103440400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr4:103439000-103440400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr4:103439200-103440200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr4:103439200-103440200	Enhancers	Rectal Smooth Muscle	rectum
42	chr4:103439200-103441200	Enhancers	Adipose Nuclei	Adipose
43	chr4:103439200-103441400	Enhancers	Brain Cingulate Gyrus	brain
44	chr4:103439200-103441400	Enhancers	Brain Hippocampus Middle	brain
45	chr4:103439200-103441400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr4:103439400-103440200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
47	chr4:103439400-103440200	Enhancers	Brain Angular Gyrus	brain
48	chr4:103439400-103440200	Enhancers	Colon Smooth Muscle	Colon
49	chr4:103439400-103440200	Enhancers	HepG2	liver
50	chr4:103439400-103440400	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links