Variant report

Variant	rs9308813
Chromosome Location	chr2:99263380-99263381
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	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]
rs10189698	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]
rs1028144	0.96[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11123746	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs12468113	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613547	0.82[EUR][1000 genomes]
rs12613577	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12616821	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1514914	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1599827	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1599828	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17448190	1.00[YRI][hapmap]
rs2063780	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2271670	0.96[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2309432	0.82[EUR][1000 genomes]
rs2309433	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2871234	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs34457904	0.82[EUR][1000 genomes]
rs34622150	0.81[EUR][1000 genomes]
rs3754870	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]
rs3769689	1.00[YRI][hapmap]
rs3769691	0.88[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4508652	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4513341	0.81[EUR][1000 genomes]
rs6542835	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]
rs6719489	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs6750281	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7557647	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs9308814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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:69 , 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	chr2:99234800-99264600	Weak transcription	Ovary	ovary
4	chr2:99234800-99296400	Weak transcription	Esophagus	oesophagus
5	chr2:99235400-99273600	Weak transcription	Fetal Kidney	kidney
6	chr2:99243600-99265800	Strong transcription	Duodenum Mucosa	Duodenum
7	chr2:99244200-99265600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:99244800-99265400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:99245000-99268000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:99247200-99265600	Strong transcription	HepG2	liver
11	chr2:99249800-99265600	Weak transcription	Brain Substantia Nigra	brain
12	chr2:99249800-99318000	Weak transcription	Psoas Muscle	Psoas
13	chr2:99251200-99263600	Weak transcription	Placenta	Placenta
14	chr2:99251400-99269000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:99251400-99277800	Weak transcription	Spleen	Spleen
16	chr2:99251400-99295600	Weak transcription	Fetal Stomach	stomach
17	chr2:99251600-99264200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:99251600-99264200	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:99251600-99275400	Weak transcription	Gastric	stomach
20	chr2:99251600-99302000	Weak transcription	Brain Angular Gyrus	brain
21	chr2:99251600-99306600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:99251800-99275600	Weak transcription	Aorta	Aorta
23	chr2:99252200-99271200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:99253200-99277400	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:99253200-99293000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:99253600-99265000	Weak transcription	Brain Anterior Caudate	brain
27	chr2:99254400-99264000	Weak transcription	Thymus	Thymus
28	chr2:99254600-99264000	Weak transcription	Pancreas	Pancrea
29	chr2:99254600-99265600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:99254600-99265800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:99255200-99265800	Strong transcription	Dnd41	blood
32	chr2:99255600-99264200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:99255600-99265000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:99255600-99265000	Strong transcription	Fetal Thymus	thymus
35	chr2:99255600-99265400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:99255600-99265800	Strong transcription	Fetal Intestine Large	intestine
37	chr2:99255600-99306800	Weak transcription	Colonic Mucosa	Colon
38	chr2:99255800-99264800	Strong transcription	Primary T cells from cord blood	blood
39	chr2:99255800-99265000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:99256000-99263800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:99256400-99296000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:99256600-99271000	Weak transcription	Primary B cells from cord blood	blood
43	chr2:99257600-99264000	Weak transcription	Adipose Nuclei	Adipose
44	chr2:99258200-99265800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:99258600-99265800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:99258800-99265400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:99259000-99263800	Weak transcription	Lung	lung
48	chr2:99259000-99265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:99259000-99281800	Weak transcription	Left Ventricle	heart
50	chr2:99259200-99264000	Weak transcription	Fetal Intestine Small	intestine

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