Variant report

Variant	rs2038053
Chromosome Location	chr1:209920538-209920539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209920122..209922907-chr1:209973621..209976183,2	MCF-7	breast:
2	chr1:209897489..209898995-chr1:209918699..209920810,2	K562	blood:
3	chr1:209913450..209916086-chr1:209919671..209921571,2	K562	blood:
4	chr1:209916474..209918920-chr1:209920104..209922211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000236136	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10082248	1.00[CEU][hapmap]
rs10489343	1.00[AFR][1000 genomes]
rs10779514	1.00[AFR][1000 genomes]
rs10779515	1.00[AFR][1000 genomes]
rs10863789	1.00[AFR][1000 genomes]
rs10863790	1.00[AFR][1000 genomes]
rs1109430	1.00[AFR][1000 genomes]
rs11119345	0.85[EUR][1000 genomes]
rs11119347	1.00[AFR][1000 genomes]
rs11119348	1.00[AFR][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12058100	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes]
rs12081405	1.00[AFR][1000 genomes]
rs12405750	1.00[AFR][1000 genomes]
rs12561766	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015076	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17015078	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17015255	1.00[AFR][1000 genomes]
rs17015268	1.00[AFR][1000 genomes]
rs17388240	1.00[AFR][1000 genomes]
rs1856161	1.00[AFR][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2076149	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2076151	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2235370	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2235371	1.00[AFR][1000 genomes]
rs2235377	1.00[AFR][1000 genomes]
rs2236902	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2272866	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2282740	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294406	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298930	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3753517	1.00[AFR][1000 genomes]
rs41274836	1.00[AFR][1000 genomes]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs4545339	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844488	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4844491	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4844494	1.00[AFR][1000 genomes]
rs4844496	1.00[AFR][1000 genomes]
rs4844893	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4844894	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs56822893	0.85[EUR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58788672	0.83[EUR][1000 genomes]
rs6540547	1.00[CEU][hapmap]
rs6694238	1.00[CEU][hapmap]
rs7515014	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7517461	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528642	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532021	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs846908	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209907600-209920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209915200-209920800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:209915200-209921000	Weak transcription	Spleen	Spleen
4	chr1:209915400-209920800	Weak transcription	Esophagus	oesophagus
5	chr1:209915600-209920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:209916000-209920800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:209916000-209920800	Weak transcription	GM12878-XiMat	blood
8	chr1:209916800-209920800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:209916800-209920800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:209916800-209920800	Weak transcription	Left Ventricle	heart
11	chr1:209917000-209920600	Weak transcription	Brain Anterior Caudate	brain
12	chr1:209917000-209920800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:209917000-209920800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:209917200-209920600	Weak transcription	Osteobl	bone
15	chr1:209917200-209920800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:209917200-209920800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr1:209917200-209920800	Weak transcription	Liver	Liver
18	chr1:209917200-209920800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:209917200-209920800	Weak transcription	NH-A	brain
20	chr1:209917200-209920800	Weak transcription	NHLF	lung
21	chr1:209917800-209920800	Weak transcription	Pancreas	Pancrea
22	chr1:209917800-209920800	Weak transcription	Right Atrium	heart
23	chr1:209917800-209920800	Weak transcription	Right Ventricle	heart
24	chr1:209918400-209920800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:209919400-209920800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:209919400-209921000	Enhancers	Fetal Intestine Large	intestine
27	chr1:209919600-209920600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:209919600-209920800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:209919600-209920800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:209919600-209922400	Enhancers	Fetal Heart	heart
31	chr1:209919800-209920600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:209919800-209920800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:209919800-209920800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:209919800-209921000	Weak transcription	Thymus	Thymus
35	chr1:209919800-209923400	Enhancers	Fetal Intestine Small	intestine
36	chr1:209920000-209920800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:209920000-209920800	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:209920000-209920800	Enhancers	Stomach Mucosa	stomach
39	chr1:209920000-209920800	Enhancers	K562	blood
40	chr1:209920200-209920800	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:209920200-209920800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:209920200-209920800	Enhancers	Adipose Nuclei	Adipose
43	chr1:209920200-209920800	Enhancers	Brain Substantia Nigra	brain
44	chr1:209920400-209920600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:209920400-209920800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:209920400-209920800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:209920400-209920800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:209920400-209920800	Enhancers	Brain Angular Gyrus	brain
49	chr1:209920400-209920800	Enhancers	Brain Hippocampus Middle	brain
50	chr1:209920400-209920800	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links