Variant report

Variant	rs3754870
Chromosome Location	chr2:99272057-99272058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10189698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1028144	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123746	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs11679648	0.84[ASW][hapmap]
rs12467276	0.86[ASW][hapmap]
rs12468086	0.86[ASW][hapmap]
rs12468113	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12613547	0.84[EUR][1000 genomes]
rs12613577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12616821	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1514914	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1599827	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1599828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17448190	1.00[YRI][hapmap]
rs17448420	0.86[ASW][hapmap]
rs17514013	0.86[ASW][hapmap]
rs2063780	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2271670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2309432	0.84[EUR][1000 genomes]
rs2309433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871234	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs34457904	0.84[EUR][1000 genomes]
rs34622150	0.83[EUR][1000 genomes]
rs3769688	0.86[ASW][hapmap]
rs3769689	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs3769691	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508652	0.82[EUR][1000 genomes]
rs4513341	0.82[EUR][1000 genomes]
rs6542835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6750281	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7557647	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs9308813	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9308814	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]

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	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv582516	chr2:99254031-99304794	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99231200-99286200	Weak transcription	Stomach Mucosa	stomach
2	chr2:99234600-99310600	Weak transcription	Small Intestine	intestine
3	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
4	chr2:99235400-99273600	Weak transcription	Fetal Kidney	kidney
5	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
6	chr2:99251400-99277800	Weak transcription	Spleen	Spleen
7	chr2:99251400-99295600	Weak transcription	Fetal Stomach	stomach
8	chr2:99251600-99275400	Weak transcription	Gastric	stomach
9	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:99251800-99275600	Weak transcription	Aorta	Aorta
12	chr2:99253200-99277400	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:99253200-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
15	chr2:99256400-99296000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:99259000-99281800	Weak transcription	Left Ventricle	heart
17	chr2:99260000-99288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:99260600-99290400	Weak transcription	Liver	Liver
19	chr2:99260600-99290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:99264600-99299000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:99265200-99275400	Weak transcription	Pancreas	Pancrea
22	chr2:99265200-99291800	Weak transcription	Placenta	Placenta
23	chr2:99265400-99290800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:99265600-99306600	Weak transcription	Lung	lung
25	chr2:99265800-99275400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:99265800-99303800	Weak transcription	Brain Substantia Nigra	brain
27	chr2:99266200-99290400	Weak transcription	Adipose Nuclei	Adipose
28	chr2:99266200-99296200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:99266400-99275400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:99266400-99278000	Weak transcription	HUVEC	blood vessel
31	chr2:99266400-99304200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:99267400-99272800	Weak transcription	Fetal Intestine Large	intestine
33	chr2:99267600-99284200	Weak transcription	Fetal Intestine Small	intestine
34	chr2:99268000-99273000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:99268600-99273400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:99269000-99273400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:99269400-99272800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:99269600-99272600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:99269600-99277000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:99270000-99272200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr2:99270200-99272600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:99270400-99273400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:99270600-99272200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:99270600-99274400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr2:99270600-99293800	Strong transcription	HepG2	liver
46	chr2:99271000-99273000	Enhancers	Primary B cells from cord blood	blood
47	chr2:99271200-99272200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr2:99271200-99272400	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:99271200-99272400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr2:99271200-99272600	Genic enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links