Variant report

Variant	rs10189698
Chromosome Location	chr2:99265241-99265242
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99257483..99259100-chr2:99264246..99265967,2	MCF-7	breast:
2	chr2:99260976..99264439-chr2:99264618..99267793,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1028144	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1599828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17448190	1.00[YRI][hapmap]
rs2063780	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs2271670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3769689	1.00[YRI][hapmap]
rs3769691	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4508652	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4513341	0.82[EUR][1000 genomes]
rs6542835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6750281	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[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];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9308814	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[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:70 , 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	chr2:99243600-99265800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:99244200-99265600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:99244800-99265400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:99245000-99268000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:99247200-99265600	Strong transcription	HepG2	liver
10	chr2:99249800-99265600	Weak transcription	Brain Substantia Nigra	brain
11	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
12	chr2:99251400-99269000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:99251400-99277800	Weak transcription	Spleen	Spleen
14	chr2:99251400-99295600	Weak transcription	Fetal Stomach	stomach
15	chr2:99251600-99275400	Weak transcription	Gastric	stomach
16	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
17	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:99251800-99275600	Weak transcription	Aorta	Aorta
19	chr2:99252200-99271200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:99253200-99277400	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:99253200-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:99254600-99265600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:99254600-99265800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:99255200-99265800	Strong transcription	Dnd41	blood
25	chr2:99255600-99265400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:99255600-99265800	Strong transcription	Fetal Intestine Large	intestine
27	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
28	chr2:99256400-99296000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:99256600-99271000	Weak transcription	Primary B cells from cord blood	blood
30	chr2:99258200-99265800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:99258600-99265800	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:99258800-99265400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:99259000-99281800	Weak transcription	Left Ventricle	heart
34	chr2:99260000-99288000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:99260600-99290400	Weak transcription	Liver	Liver
36	chr2:99260600-99290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:99260800-99265800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:99262600-99265800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:99263800-99265600	Strong transcription	Lung	lung
40	chr2:99263800-99265600	Strong transcription	HUVEC	blood vessel
41	chr2:99263800-99265800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:99264000-99265600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:99264000-99265800	Strong transcription	Fetal Intestine Small	intestine
44	chr2:99264000-99265800	Strong transcription	Thymus	Thymus
45	chr2:99264000-99266000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:99264200-99265400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:99264200-99265400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:99264200-99265400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr2:99264200-99265800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:99264200-99265800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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