Variant report

Variant	rs2174683
Chromosome Location	chr4:102087011-102087012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:50527951..50530395-chr4:102085394..102088001,2	MCF-7	breast:
2	chr4:102086824..102091694-chr4:102266945..102270646,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138814	Chromatin interaction
ENSG00000254531	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1021965	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1354785	0.80[ASN][1000 genomes]
rs1395475	0.80[ASN][1000 genomes]
rs1395476	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1506799	0.80[ASN][1000 genomes]
rs1506800	0.80[ASN][1000 genomes]
rs1506802	0.80[ASN][1000 genomes]
rs1506803	0.80[ASN][1000 genomes]
rs1506804	0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543856	0.80[ASN][1000 genomes]
rs17030851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2135610	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135614	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659503	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659504	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659505	0.82[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2659506	0.82[GIH][hapmap];0.85[JPT][hapmap]
rs2659508	0.84[CHD][hapmap];0.82[GIH][hapmap];0.82[ASN][1000 genomes]
rs2659509	0.82[GIH][hapmap]
rs2659511	0.82[GIH][hapmap]
rs2659512	0.80[ASN][1000 genomes]
rs2659513	0.80[ASN][1000 genomes]
rs2659533	0.82[GIH][hapmap]
rs2659534	0.82[GIH][hapmap]
rs2659539	0.80[ASN][1000 genomes]
rs2659540	0.80[ASN][1000 genomes]
rs2659541	0.80[ASN][1000 genomes]
rs2850980	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850981	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850982	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850985	0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2850987	0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2850989	0.80[ASN][1000 genomes]
rs2850991	0.80[ASN][1000 genomes]
rs2850994	0.80[CHD][hapmap]
rs4478191	0.85[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58879959	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73833252	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs931871	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2760883	chr4:102081357-102088150	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102062600-102090400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:102078400-102093200	Weak transcription	HUVEC	blood vessel
3	chr4:102078400-102096600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:102078600-102088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:102078600-102090200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:102078800-102096000	Weak transcription	Ovary	ovary
7	chr4:102079000-102088800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:102079400-102113800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:102079600-102088800	Weak transcription	Psoas Muscle	Psoas
10	chr4:102079800-102087200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:102079800-102096400	Weak transcription	Adipose Nuclei	Adipose
12	chr4:102080000-102092200	Weak transcription	NHDF-Ad	bronchial
13	chr4:102080000-102092600	Weak transcription	NH-A	brain
14	chr4:102080400-102087400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:102080400-102088800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:102080600-102093000	Weak transcription	NHLF	lung
17	chr4:102080600-102100600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:102081000-102090200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:102082600-102090000	Weak transcription	Primary B cells from cord blood	blood
20	chr4:102083000-102088400	Weak transcription	Brain Anterior Caudate	brain
21	chr4:102083000-102096200	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:102083200-102096800	Weak transcription	Brain Angular Gyrus	brain
23	chr4:102083800-102087200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:102084000-102089200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:102084200-102088800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:102084200-102103400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:102084600-102089400	Weak transcription	Brain Substantia Nigra	brain
28	chr4:102084800-102090200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:102084800-102092000	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:102085400-102090400	Weak transcription	Esophagus	oesophagus
31	chr4:102085400-102094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:102085600-102096600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:102085800-102088000	Weak transcription	HMEC	breast
34	chr4:102086000-102088000	Weak transcription	NHEK	skin
35	chr4:102086000-102088200	Weak transcription	Small Intestine	intestine
36	chr4:102086400-102088000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:102086400-102088000	Weak transcription	A549	lung
38	chr4:102086800-102087200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr4:102086800-102087200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr4:102086800-102087600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr4:102086800-102089800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:102087000-102087600	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:102087000-102087800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links