Variant report

Variant	rs3813250
Chromosome Location	chr2:179395958-179395959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179395497..179400266-chr2:179412543..179417721,4	K562	blood:
2	chr2:179395770..179398427-chr2:179417927..179420746,2	K562	blood:
3	chr2:179386919..179391089-chr2:179391647..179398872,11	K562	blood:
4	chr2:179386627..179389310-chr2:179394176..179396606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237298	Chromatin interaction
ENSG00000270277	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1001238	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930831	0.82[CHB][hapmap]
rs12693162	0.94[ASW][hapmap];0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13411588	0.82[CHB][hapmap]
rs1560221	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16866400	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs16866420	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2042995	0.94[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs2042996	0.82[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2163009	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288322	0.81[CHB][hapmap]
rs2288571	0.81[JPT][hapmap]
rs2303838	0.81[JPT][hapmap]
rs2366751	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472751	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562845	0.85[TSI][hapmap]
rs2742351	0.86[CHB][hapmap]
rs35504893	0.94[ASN][1000 genomes]
rs36113194	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3731746	0.81[JPT][hapmap]
rs3731750	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731754	0.80[CHB][hapmap]
rs3752689	0.82[CHB][hapmap]
rs3769864	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769866	0.81[CHB][hapmap]
rs3820978	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829746	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894020	0.82[CHB][hapmap]
rs4894029	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4894030	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs6704545	0.81[CHB][hapmap]
rs6712785	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6723399	0.87[ASN][1000 genomes]
rs6735077	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6739142	0.82[CHB][hapmap]
rs6753709	0.86[CHB][hapmap]
rs7600176	0.86[CHB][hapmap]
rs8179648	0.85[JPT][hapmap]
rs890578	0.81[JPT][hapmap]
rs957875	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs967507	0.81[CHB][hapmap]
rs9808377	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS 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	nsv522036	chr2:179395760-179398509	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3813250	HOXD9	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179396000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:179388800-179396200	Weak transcription	Fetal Kidney	kidney
3	chr2:179388800-179396200	Weak transcription	Gastric	stomach
4	chr2:179388800-179396200	Weak transcription	Pancreas	Pancrea
5	chr2:179388800-179403600	Weak transcription	Esophagus	oesophagus
6	chr2:179388800-179408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:179388800-179408600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:179388800-179410600	Weak transcription	Colonic Mucosa	Colon
9	chr2:179388800-179411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:179388800-179417600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
14	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:179389000-179396000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:179389000-179396000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:179389000-179396000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:179389000-179396200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:179389000-179396200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:179389000-179396200	Weak transcription	Fetal Brain Female	brain
21	chr2:179389200-179396200	Weak transcription	Brain Anterior Caudate	brain
22	chr2:179389200-179396200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:179389200-179412600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:179389400-179396000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:179389400-179396000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:179389400-179396000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:179389400-179396000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:179389400-179396000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:179389400-179396000	Weak transcription	Fetal Lung	lung
30	chr2:179389400-179396000	Weak transcription	Ovary	ovary
31	chr2:179389400-179396000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:179389400-179396000	Weak transcription	A549	lung
33	chr2:179389400-179396200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:179389400-179396200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:179389400-179396200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:179389400-179396200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:179389400-179396200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:179389400-179396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:179389400-179396200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:179389400-179396200	Weak transcription	Liver	Liver
41	chr2:179389400-179396200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:179389400-179396200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:179389400-179396200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:179389400-179396200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:179389400-179396200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:179389400-179396200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:179389400-179396200	Weak transcription	Thymus	Thymus
48	chr2:179389400-179396200	Weak transcription	NHEK	skin
49	chr2:179389400-179396200	Weak transcription	Osteobl	bone
50	chr2:179389400-179396400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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