Variant report

Variant	rs2540919
Chromosome Location	chr2:37112358-37112359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37112041..37114418-chr22:37594275..37597076,2	MCF-7	breast:
2	chr2:37110942..37112649-chr2:37193437..37195294,2	MCF-7	breast:
3	chr2:37112252..37114608-chr2:37115570..37119781,3	MCF-7	breast:
4	chr2:37111890..37113424-chr2:37118017..37119870,2	K562	blood:

Variant related genes	Relation type
ENSG00000115808	Chromatin interaction
ENSG00000133466	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10164948	0.80[EUR][1000 genomes]
rs10166161	0.80[EUR][1000 genomes]
rs10176081	0.80[EUR][1000 genomes]
rs10176124	0.80[EUR][1000 genomes]
rs10180003	0.80[EUR][1000 genomes]
rs10182741	0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs10183626	0.81[EUR][1000 genomes]
rs10185737	0.88[EUR][1000 genomes]
rs10189328	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10189918	0.88[EUR][1000 genomes]
rs10201963	0.86[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10202311	0.88[EUR][1000 genomes]
rs1043290	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10490659	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs10495868	0.86[CHB][hapmap]
rs11124552	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs11673811	0.80[EUR][1000 genomes]
rs11674211	0.86[CHB][hapmap]
rs11675109	0.86[CHB][hapmap]
rs11676225	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs11678303	0.86[CHB][hapmap];0.92[ASN][1000 genomes]
rs11678807	0.80[EUR][1000 genomes]
rs11680617	0.80[EUR][1000 genomes]
rs11680663	0.80[EUR][1000 genomes]
rs11682966	0.86[CHB][hapmap];0.96[ASN][1000 genomes]
rs11685600	0.88[EUR][1000 genomes]
rs11904023	0.86[CHB][hapmap]
rs12328274	0.83[ASN][1000 genomes]
rs12479195	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12624290	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13385627	0.81[ASN][1000 genomes]
rs13388406	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401327	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13408941	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13413438	0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs13432707	0.80[EUR][1000 genomes]
rs17020005	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs17020024	0.96[ASN][1000 genomes]
rs17020069	0.86[CHB][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs17020072	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs17020074	0.86[CHB][hapmap]
rs17020084	0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs17442690	0.85[ASN][1000 genomes]
rs17442739	0.85[ASN][1000 genomes]
rs1861433	0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1861434	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1861436	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2041828	0.81[EUR][1000 genomes]
rs2160379	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2216106	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255330	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2287087	0.85[ASN][1000 genomes]
rs2302658	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2372812	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2540918	1.00[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2540920	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2540925	0.91[ASN][1000 genomes]
rs2540931	0.91[ASN][1000 genomes]
rs2540936	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691104	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691109	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691110	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691114	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2691115	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691116	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2691118	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691122	0.86[ASN][1000 genomes]
rs2717492	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2717494	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2717495	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2717496	0.82[ASN][1000 genomes]
rs2717500	0.83[ASN][1000 genomes]
rs2717501	0.86[CHB][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs2717505	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2717508	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2717509	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2717510	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2717511	0.86[CHB][hapmap]
rs2717512	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2717516	0.93[ASN][1000 genomes]
rs2717518	0.86[CHB][hapmap];0.96[ASN][1000 genomes]
rs2717519	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2717520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2717522	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28718824	0.86[CHB][hapmap];0.83[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28754306	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2888418	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35622893	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770775	0.86[CHB][hapmap]
rs3845779	0.86[CHB][hapmap]
rs41486347	0.86[CHB][hapmap];0.91[ASN][1000 genomes]
rs4635515	0.86[CHB][hapmap]
rs55993128	0.92[ASN][1000 genomes]
rs56186144	0.92[ASN][1000 genomes]
rs57671539	0.92[ASN][1000 genomes]
rs57884362	0.98[ASN][1000 genomes]
rs58970461	0.92[ASN][1000 genomes]
rs6715033	0.91[ASN][1000 genomes]
rs6739553	0.96[ASN][1000 genomes]
rs6756876	0.91[ASN][1000 genomes]
rs6759472	0.81[EUR][1000 genomes]
rs723673	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73924932	0.83[ASN][1000 genomes]
rs7562109	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7579735	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7581702	0.86[CHB][hapmap]
rs9789527	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs998321	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv456363	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv581470	chr2:37109281-37235324	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37067600-37146200	Weak transcription	Psoas Muscle	Psoas
2	chr2:37075600-37139200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:37077000-37116200	Weak transcription	Hela-S3	cervix
4	chr2:37077000-37116200	Weak transcription	NHLF	lung
5	chr2:37077200-37144400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:37077400-37136600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:37078200-37118400	Weak transcription	Fetal Brain Male	brain
8	chr2:37082200-37115600	Weak transcription	Stomach Mucosa	stomach
9	chr2:37087400-37146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:37090800-37114200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:37091000-37114000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:37091200-37114400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:37092800-37115600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:37094200-37113400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:37094400-37154200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:37095800-37112600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:37096400-37117000	Weak transcription	K562	blood
18	chr2:37096400-37143800	Weak transcription	Fetal Kidney	kidney
19	chr2:37096800-37154400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:37098000-37112400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:37099000-37116800	Weak transcription	A549	lung
22	chr2:37099200-37140200	Weak transcription	Colonic Mucosa	Colon
23	chr2:37099600-37112400	Weak transcription	HUVEC	blood vessel
24	chr2:37100400-37116800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:37101800-37119200	Weak transcription	GM12878-XiMat	blood
26	chr2:37102400-37114200	Weak transcription	NHDF-Ad	bronchial
27	chr2:37103800-37113400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:37103800-37117200	Weak transcription	HSMMtube	muscle
29	chr2:37103800-37121400	Weak transcription	Small Intestine	intestine
30	chr2:37103800-37146200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:37104200-37117800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:37105000-37152600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr2:37105000-37164600	Weak transcription	Lung	lung
34	chr2:37105200-37115200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:37105200-37116600	Weak transcription	NHEK	skin
36	chr2:37105200-37117000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:37105200-37117200	Weak transcription	HMEC	breast
38	chr2:37105200-37118400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:37105200-37125400	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:37105200-37136200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:37105200-37139200	Weak transcription	Aorta	Aorta
42	chr2:37105200-37141200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:37105200-37144000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:37105200-37154400	Weak transcription	Esophagus	oesophagus
45	chr2:37105200-37157800	Weak transcription	Pancreas	Pancrea
46	chr2:37105200-37164600	Weak transcription	Spleen	Spleen
47	chr2:37105800-37116800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:37105800-37146400	Weak transcription	Right Ventricle	heart
49	chr2:37106800-37113800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:37107200-37114000	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links