Variant report

Variant	rs4240341
Chromosome Location	chr4:148787669-148787670
allele	A/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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:148547064..148547916-chr4:148787644..148788200,2	MCF-7	breast:
2	chr4:148628975..148629992-chr4:148787437..148788720,7	MCF-7	breast:
3	chr4:148605054..148606838-chr4:148786766..148789557,2	MCF-7	breast:
4	chr4:148515225..148515917-chr4:148787582..148788630,4	MCF-7	breast:
5	chr4:148599912..148600517-chr4:148787659..148788439,3	MCF-7	breast:
6	chr4:147939970..147940883-chr4:148787667..148788628,4	K562	blood:
7	chr20:58508769..58509347-chr4:148787638..148788516,2	MCF-7	breast:
8	chr4:148439677..148440826-chr4:148787272..148788626,10	K562	blood:
9	chr4:148613328..148614734-chr4:148787640..148788623,7	MCF-7	breast:
10	chr4:148628378..148630020-chr4:148787161..148788732,34	MCF-7	breast:
11	chr4:148629250..148629859-chr4:148787588..148788271,2	K562	blood:
12	chr4:148602747..148604694-chr4:148786468..148788057,2	MCF-7	breast:
13	chr4:148509882..148511690-chr4:148787031..148789794,2	MCF-7	breast:
14	chr4:148604484..148605001-chr4:148787305..148788147,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164169	Chromatin interaction
ENSG00000196227	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10000278	0.98[EUR][1000 genomes]
rs10001688	0.90[EUR][1000 genomes]
rs10001756	0.92[EUR][1000 genomes]
rs10003507	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10004138	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs10004691	0.90[EUR][1000 genomes]
rs10004792	1.00[CEU][hapmap];0.85[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10014593	0.86[EUR][1000 genomes]
rs10014696	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes]
rs10015875	0.92[EUR][1000 genomes]
rs10018820	1.00[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs10018903	0.82[CEU][hapmap]
rs10025069	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs10026985	1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs10030358	1.00[CEU][hapmap];0.82[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10049932	1.00[CEU][hapmap];0.85[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs11099671	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11099672	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs11734553	0.83[EUR][1000 genomes]
rs11735412	1.00[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11737346	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12331562	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12498257	0.94[GIH][hapmap]
rs12509618	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs12513192	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12641291	0.82[CEU][hapmap]
rs12643550	0.87[EUR][1000 genomes]
rs12650219	0.82[CEU][hapmap]
rs13129325	1.00[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13151898	0.90[EUR][1000 genomes]
rs1369958	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes]
rs1469865	0.94[GIH][hapmap]
rs17024037	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs17613979	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes]
rs17614025	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs17676080	1.00[CEU][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2043643	0.94[EUR][1000 genomes]
rs2043644	0.82[CEU][hapmap]
rs2043645	0.90[EUR][1000 genomes]
rs28576385	0.92[EUR][1000 genomes]
rs28614116	0.90[EUR][1000 genomes]
rs2884400	0.92[EUR][1000 genomes]
rs34970355	0.83[EUR][1000 genomes]
rs35243600	0.90[EUR][1000 genomes]
rs35810358	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35899247	0.90[EUR][1000 genomes]
rs3893175	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3990920	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs4240338	0.82[CEU][hapmap]
rs4240339	0.82[CEU][hapmap]
rs4491995	1.00[CEU][hapmap];0.82[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs4571312	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4627844	0.83[EUR][1000 genomes]
rs4835103	0.82[CEU][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4835109	0.82[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs4835110	0.87[EUR][1000 genomes]
rs4835463	0.92[YRI][hapmap]
rs4835469	0.82[CEU][hapmap];0.81[CHD][hapmap]
rs55650760	0.80[EUR][1000 genomes]
rs55820558	0.94[EUR][1000 genomes]
rs62330732	0.89[EUR][1000 genomes]
rs62330735	0.89[EUR][1000 genomes]
rs62330737	0.85[EUR][1000 genomes]
rs6535569	0.83[EUR][1000 genomes]
rs6811769	0.83[EUR][1000 genomes]
rs6818371	1.00[CEU][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs6832527	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6840771	1.00[CEU][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs6843392	1.00[CEU][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs6846899	0.83[GIH][hapmap]
rs6856273	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7654433	0.94[GIH][hapmap]
rs7656471	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7660508	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7666127	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7677632	0.90[EUR][1000 genomes]
rs7698670	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs893022	0.82[CEU][hapmap]
rs893033	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9991741	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9994650	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs9995896	0.82[CEU][hapmap]
rs9995956	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs9996108	0.82[CEU][hapmap]
rs9996209	0.80[EUR][1000 genomes]
rs9997027	1.00[CEU][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes]
rs9999321	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2030047	chr4:148787669-148787670	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148763200-148796200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:148764600-148787800	Weak transcription	HMEC	breast
3	chr4:148766600-148796200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:148767600-148796400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:148768400-148815600	Weak transcription	Primary T cells from cord blood	blood
6	chr4:148770400-148796200	Weak transcription	Fetal Kidney	kidney
7	chr4:148772000-148806000	Weak transcription	Fetal Thymus	thymus
8	chr4:148777000-148796200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:148777000-148823000	Weak transcription	Small Intestine	intestine
10	chr4:148777400-148796600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:148777800-148796200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:148779800-148793800	Weak transcription	Fetal Lung	lung
13	chr4:148782000-148799400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:148782800-148787800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:148783000-148796200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:148783000-148796200	Weak transcription	Thymus	Thymus
17	chr4:148783400-148796400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr4:148783400-148796400	Weak transcription	Lung	lung
19	chr4:148783600-148789800	Weak transcription	Fetal Intestine Small	intestine
20	chr4:148783600-148796200	Weak transcription	Esophagus	oesophagus
21	chr4:148783600-148796200	Weak transcription	Placenta	Placenta
22	chr4:148783800-148788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:148783800-148788400	Weak transcription	Fetal Stomach	stomach
24	chr4:148783800-148789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:148783800-148790000	Weak transcription	Left Ventricle	heart
26	chr4:148783800-148796200	Weak transcription	Fetal Intestine Large	intestine
27	chr4:148783800-148796200	Weak transcription	Gastric	stomach
28	chr4:148783800-148796200	Weak transcription	Right Ventricle	heart
29	chr4:148784200-148788400	Enhancers	Colon Smooth Muscle	Colon
30	chr4:148784400-148810800	Weak transcription	Fetal Heart	heart
31	chr4:148784600-148796400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:148785400-148796200	Weak transcription	GM12878-XiMat	blood
33	chr4:148785600-148788400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:148785600-148796200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:148785800-148787800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:148786000-148788200	Weak transcription	NHDF-Ad	bronchial
37	chr4:148786000-148788400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:148786000-148788600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr4:148786000-148789800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:148786000-148790200	Strong transcription	HSMM	muscle
41	chr4:148786000-148804000	Weak transcription	Psoas Muscle	Psoas
42	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
43	chr4:148786200-148788000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:148786400-148788400	Weak transcription	Adipose Nuclei	Adipose
45	chr4:148786400-148788400	Weak transcription	Fetal Muscle Leg	muscle
46	chr4:148786400-148796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:148786600-148788600	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr4:148786800-148788000	Enhancers	HUVEC	blood vessel
49	chr4:148786800-148788200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr4:148786800-148788600	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links