Variant report

Variant	rs6542835
Chromosome Location	chr2:99267946-99267947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10189698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1028144	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123746	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs12468113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[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];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12616821	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1514914	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1599827	0.92[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063780	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs2271670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[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];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871234	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs34457904	0.84[EUR][1000 genomes]
rs34622150	0.83[EUR][1000 genomes]
rs3754870	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]
rs3769691	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508652	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4513341	0.82[EUR][1000 genomes]
rs6719489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6750281	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7557647	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs9308813	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9308814	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][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:67 , 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	chr2:99245000-99268000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
7	chr2:99251400-99269000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:99251400-99277800	Weak transcription	Spleen	Spleen
9	chr2:99251400-99295600	Weak transcription	Fetal Stomach	stomach
10	chr2:99251600-99275400	Weak transcription	Gastric	stomach
11	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
12	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:99251800-99275600	Weak transcription	Aorta	Aorta
14	chr2:99252200-99271200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:99253200-99277400	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:99253200-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
18	chr2:99256400-99296000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:99256600-99271000	Weak transcription	Primary B cells from cord blood	blood
20	chr2:99259000-99281800	Weak transcription	Left Ventricle	heart
21	chr2:99260000-99288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:99260600-99290400	Weak transcription	Liver	Liver
23	chr2:99260600-99290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:99264600-99270600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:99264600-99299000	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:99265200-99275400	Weak transcription	Pancreas	Pancrea
27	chr2:99265200-99291800	Weak transcription	Placenta	Placenta
28	chr2:99265400-99270000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:99265400-99270600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:99265400-99271600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:99265400-99271800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:99265400-99290800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:99265600-99271200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:99265600-99306600	Weak transcription	Lung	lung
35	chr2:99265800-99270000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:99265800-99270400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:99265800-99271200	Weak transcription	Thymus	Thymus
38	chr2:99265800-99271400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr2:99265800-99275400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:99265800-99303800	Weak transcription	Brain Substantia Nigra	brain
41	chr2:99266000-99269200	Weak transcription	NHEK	skin
42	chr2:99266200-99290400	Weak transcription	Adipose Nuclei	Adipose
43	chr2:99266200-99296200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:99266400-99268200	Weak transcription	Brain Anterior Caudate	brain
45	chr2:99266400-99269600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:99266400-99271200	Weak transcription	Fetal Thymus	thymus
47	chr2:99266400-99271400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:99266400-99275400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:99266400-99278000	Weak transcription	HUVEC	blood vessel
50	chr2:99266400-99304200	Weak transcription	Brain Inferior Temporal Lobe	brain

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