Variant report

Variant	rs12104902
Chromosome Location	chr2:55543518-55543519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10183953	0.82[JPT][hapmap]
rs10209598	1.00[ASN][1000 genomes]
rs10439479	0.82[JPT][hapmap]
rs10496041	1.00[CEU][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125562	1.00[ASN][1000 genomes]
rs11694920	0.82[JPT][hapmap]
rs11892007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11904107	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12105322	1.00[ASN][1000 genomes]
rs12105731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12617316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13016664	1.00[ASN][1000 genomes]
rs13031346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13407931	1.00[ASN][1000 genomes]
rs1437387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1437388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1437389	0.82[JPT][hapmap]
rs1437392	0.82[JPT][hapmap]
rs1545120	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1561231	0.82[JPT][hapmap]
rs17046793	1.00[CEU][hapmap]
rs17046834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2043714	0.82[JPT][hapmap]
rs2118283	0.82[JPT][hapmap]
rs2249856	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2289168	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2576691	1.00[ASN][1000 genomes]
rs2576692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2576693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2576694	0.94[ASN][1000 genomes]
rs2576697	1.00[ASN][1000 genomes]
rs2576698	1.00[ASN][1000 genomes]
rs2576699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2576702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589063	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589067	0.85[ASN][1000 genomes]
rs2589081	0.82[JPT][hapmap]
rs2589082	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2589110	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2589111	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589112	1.00[ASN][1000 genomes]
rs2589113	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2589114	1.00[ASN][1000 genomes]
rs2589115	0.85[ASN][1000 genomes]
rs2589116	1.00[ASN][1000 genomes]
rs2589117	1.00[ASN][1000 genomes]
rs2917781	0.94[ASN][1000 genomes]
rs2920959	1.00[ASN][1000 genomes]
rs2920972	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2966465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4233959	0.82[JPT][hapmap]
rs4591380	0.82[JPT][hapmap]
rs57105158	1.00[ASN][1000 genomes]
rs59554860	0.94[ASN][1000 genomes]
rs6545476	0.82[JPT][hapmap]
rs6545479	0.82[JPT][hapmap]
rs6545482	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6705991	1.00[ASN][1000 genomes]
rs6713058	0.82[JPT][hapmap]
rs6715694	0.82[JPT][hapmap]
rs6716066	0.82[JPT][hapmap]
rs6718747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs6719579	0.82[JPT][hapmap]
rs6721211	1.00[ASN][1000 genomes]
rs6723870	0.82[JPT][hapmap]
rs6726732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6733567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6740631	1.00[ASN][1000 genomes]
rs6746287	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6747682	0.82[JPT][hapmap]
rs6750501	0.82[JPT][hapmap]
rs73939905	1.00[ASN][1000 genomes]
rs749221	1.00[CEU][hapmap]
rs9784090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
5	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
6	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
9	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
10	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
14	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:55523000-55548000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
19	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:55523600-55548000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:55524800-55549400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:55526400-55549600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:55527000-55546400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:55529400-55544400	Weak transcription	Placenta	Placenta
26	chr2:55532200-55543800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:55533000-55544000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
29	chr2:55534800-55544200	Strong transcription	Liver	Liver
30	chr2:55535200-55549600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:55535200-55549600	Strong transcription	Dnd41	blood
32	chr2:55535400-55546400	Strong transcription	HepG2	liver
33	chr2:55535400-55548000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:55535400-55550200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:55536400-55548400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:55537200-55546200	Strong transcription	Fetal Lung	lung
37	chr2:55537200-55546600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:55537200-55550200	Strong transcription	HSMM	muscle
39	chr2:55537400-55549600	Strong transcription	Fetal Thymus	thymus
40	chr2:55537600-55546600	Strong transcription	Fetal Muscle Leg	muscle
41	chr2:55537600-55548600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:55537600-55550200	Strong transcription	Brain Substantia Nigra	brain
43	chr2:55537800-55546200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:55537800-55546200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr2:55537800-55554600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:55537800-55609400	Weak transcription	Lung	lung
47	chr2:55538000-55546200	Strong transcription	Brain Germinal Matrix	brain
48	chr2:55538000-55549600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:55538000-55550000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:55538400-55546800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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