Variant report

Variant	rs6710100
Chromosome Location	chr2:180010373-180010374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10497535	0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs11892241	0.87[AFR][1000 genomes]
rs11897308	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11900884	0.85[AFR][1000 genomes]
rs11901408	0.88[YRI][hapmap]
rs11901421	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11903685	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11904657	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1490997	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16866635	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16866636	0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16866647	1.00[MEX][hapmap]
rs16866665	0.84[AFR][1000 genomes]
rs16866667	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2044477	0.95[AFR][1000 genomes]
rs3731739	1.00[ASW][hapmap];0.98[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs3816345	1.00[ASW][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs6433758	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433759	0.86[AFR][1000 genomes]
rs6433762	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433763	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6433765	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6707001	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6723850	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6725309	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs6728401	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6746115	1.00[MEX][hapmap]
rs6752298	0.81[AFR][1000 genomes]
rs7566810	0.88[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7598995	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs7608106	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs930620	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3060	chr2:179990791-180035511	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:179973400-180012600	Weak transcription	NHLF	lung
4	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
7	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:179980000-180038800	Weak transcription	HMEC	breast
9	chr2:179980000-180056800	Weak transcription	HSMM	muscle
10	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:179985000-180025600	Weak transcription	Fetal Intestine Small	intestine
12	chr2:179986600-180030400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:179991600-180043200	Weak transcription	Psoas Muscle	Psoas
14	chr2:179992200-180014600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:179995800-180016200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:179996200-180047600	Weak transcription	NH-A	brain
17	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
18	chr2:180000600-180016200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:180000600-180016200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:180001200-180016200	Strong transcription	HepG2	liver
21	chr2:180002000-180011200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:180002400-180012800	Weak transcription	NHEK	skin
23	chr2:180002400-180016400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:180002400-180030200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:180003200-180011400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:180003200-180011600	Weak transcription	A549	lung
27	chr2:180003200-180039800	Weak transcription	Brain Germinal Matrix	brain
28	chr2:180003800-180016200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:180004400-180011000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:180004800-180019200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:180004800-180046000	Weak transcription	Spleen	Spleen
32	chr2:180005000-180028800	Weak transcription	Hela-S3	cervix
33	chr2:180005600-180014400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:180005600-180014600	Weak transcription	Lung	lung
35	chr2:180005600-180040200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:180005600-180044400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:180005600-180044400	Weak transcription	Esophagus	oesophagus
38	chr2:180005800-180018200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:180005800-180030200	Weak transcription	Thymus	Thymus
40	chr2:180005800-180043200	Weak transcription	Fetal Brain Male	brain
41	chr2:180005800-180053600	Weak transcription	Primary T cells from cord blood	blood
42	chr2:180006000-180014600	Weak transcription	Fetal Stomach	stomach
43	chr2:180006000-180030600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr2:180006000-180044600	Weak transcription	Pancreas	Pancrea
45	chr2:180006200-180012400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:180006200-180012600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:180006200-180014400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:180006200-180014600	Weak transcription	Gastric	stomach
49	chr2:180006200-180014800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:180006200-180016600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links