Variant report

Variant	rs230531
Chromosome Location	chr4:103450377-103450378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103449757..103452698-chr4:103468709..103470681,2	MCF-7	breast:
2	chr4:103422104..103423960-chr4:103450000..103452534,3	MCF-7	breast:
3	chr4:103422268..103425518-chr4:103448711..103450558,3	MCF-7	breast:
4	chr4:103438526..103440026-chr4:103449881..103451773,2	K562	blood:
5	chr4:103422449..103425804-chr4:103447009..103450716,4	K562	blood:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs11723120	0.87[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs118882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs12509517	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12648696	0.89[CHB][hapmap]
rs1585213	0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs1585215	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1598859	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1599961	0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs17032705	0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs170731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1801	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230493	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs230500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs230504	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs230505	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs230509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230511	1.00[CEU][hapmap]
rs230514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs230515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.97[TSI][hapmap]
rs230526	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs230528	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs230529	0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs230532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs230533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs230539	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230540	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230541	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs230542	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs3755867	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	1.00[JPT][hapmap]
rs3774936	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap]
rs3774963	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3774964	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.91[JPT][hapmap]
rs4235404	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4648011	0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs4648055	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs4648130	0.81[YRI][hapmap]
rs4648133	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4698861	0.83[CEU][hapmap]
rs4699030	0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs747559	0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs9790601	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs980455	0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs230531	BANK1	cis	parietal	SCAN
rs230531	MANBA	cis	parietal	SCAN
rs230531	CISD2	cis	parietal	SCAN
rs230531	MANBA	cis	multi-tissue	Pritchard
rs230531	ADH7	cis	cerebellum	SCAN
rs230531	COL9A2	trans	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103425200-103456400	Weak transcription	Osteobl	bone
2	chr4:103426000-103452600	Weak transcription	NH-A	brain
3	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
4	chr4:103426400-103452600	Weak transcription	HSMMtube	muscle
5	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
7	chr4:103440000-103459600	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:103440000-103460600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
10	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:103440200-103451000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:103440200-103460600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
15	chr4:103440200-103488200	Weak transcription	Gastric	stomach
16	chr4:103441400-103464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:103441400-103469400	Weak transcription	Ovary	ovary
18	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
19	chr4:103442400-103459600	Weak transcription	Fetal Stomach	stomach
20	chr4:103443000-103455400	Weak transcription	HSMM	muscle
21	chr4:103443200-103474200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:103443200-103496000	Weak transcription	A549	lung
23	chr4:103443400-103455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:103443800-103456800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:103444000-103459600	Weak transcription	Fetal Intestine Small	intestine
26	chr4:103444400-103470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:103444600-103456000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:103444800-103458600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:103444800-103473000	Weak transcription	Small Intestine	intestine
30	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:103445200-103470000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:103445600-103460400	Weak transcription	Dnd41	blood
33	chr4:103446000-103456200	Strong transcription	Primary B cells from cord blood	blood
34	chr4:103446200-103451000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:103446200-103455200	Weak transcription	Placenta	Placenta
36	chr4:103446200-103459000	Weak transcription	Left Ventricle	heart
37	chr4:103446200-103462800	Weak transcription	Esophagus	oesophagus
38	chr4:103446200-103462800	Weak transcription	Psoas Muscle	Psoas
39	chr4:103446200-103466000	Weak transcription	Lung	lung
40	chr4:103446200-103469200	Weak transcription	Pancreas	Pancrea
41	chr4:103446200-103469800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr4:103446400-103451200	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:103446400-103457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:103446600-103455200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:103446600-103466200	Weak transcription	Colon Smooth Muscle	Colon
46	chr4:103446800-103450800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:103446800-103451000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr4:103447000-103451400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:103447000-103452400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:103447200-103474000	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links