Variant report

Variant	rs12619903
Chromosome Location	chr2:55884106-55884107
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12329050	0.80[EUR][1000 genomes]
rs12467339	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12473585	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12473621	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12612227	0.82[ASN][1000 genomes]
rs12617627	0.96[YRI][hapmap]
rs12618859	0.80[CHB][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs12620407	0.88[ASN][1000 genomes]
rs12623937	0.90[CHB][hapmap]
rs12986444	0.82[ASN][1000 genomes]
rs12986797	0.82[ASN][1000 genomes]
rs12992408	0.92[YRI][hapmap]
rs12993624	0.84[JPT][hapmap];0.88[YRI][hapmap]
rs12998664	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs12998780	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12999966	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13001425	0.85[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13002860	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13005850	0.83[ASN][1000 genomes]
rs13007577	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13009447	0.83[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13009906	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs13010217	0.81[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs13013133	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13013699	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13014898	0.88[YRI][hapmap]
rs13015744	0.86[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs13019595	0.82[ASN][1000 genomes]
rs13021958	0.90[YRI][hapmap]
rs13025331	0.81[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs13027095	0.81[ASN][1000 genomes]
rs13027853	0.80[ASN][1000 genomes]
rs13032503	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs1318672	0.81[YRI][hapmap]
rs1443746	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1542643	0.80[ASN][1000 genomes]
rs17737233	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs17800203	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1822513	0.81[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2291336	0.82[ASN][1000 genomes]
rs34129478	0.82[ASN][1000 genomes]
rs34513671	0.90[AFR][1000 genomes]
rs34679603	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35124901	0.82[ASN][1000 genomes]
rs35255044	0.82[ASN][1000 genomes]
rs3791654	0.80[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs3828238	0.82[ASN][1000 genomes]
rs4322879	0.85[JPT][hapmap];0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs5012561	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs56122729	0.84[AFR][1000 genomes]
rs6737995	0.96[YRI][hapmap];0.82[ASN][1000 genomes]
rs6753530	0.86[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs6757006	0.88[CEU][hapmap];0.88[YRI][hapmap]
rs7575170	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7592219	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7596377	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs8080	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
5	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
6	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:55864400-55919600	Weak transcription	NHLF	lung
8	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
11	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
13	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
15	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55870800-55903600	Weak transcription	Gastric	stomach
17	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
19	chr2:55871000-55887800	Weak transcription	Esophagus	oesophagus
20	chr2:55871000-55893200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:55871000-55893200	Weak transcription	Thymus	Thymus
22	chr2:55871000-55920000	Weak transcription	Spleen	Spleen
23	chr2:55871200-55893400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:55871200-55905200	Weak transcription	Brain Angular Gyrus	brain
25	chr2:55871400-55905200	Weak transcription	Fetal Kidney	kidney
26	chr2:55873000-55888400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:55873200-55893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:55873200-55919800	Weak transcription	Small Intestine	intestine
29	chr2:55873800-55899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:55874800-55920200	Weak transcription	Pancreas	Pancrea
31	chr2:55875600-55887200	Weak transcription	K562	blood
32	chr2:55878800-55884400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:55879000-55888800	Strong transcription	Liver	Liver
34	chr2:55879000-55889000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:55879000-55890400	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:55879000-55891800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:55879000-55896200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:55879000-55917600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:55879200-55884200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:55879200-55884400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:55879200-55884400	Strong transcription	Hela-S3	cervix
42	chr2:55879200-55884600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:55879200-55886600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr2:55879200-55889800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:55879200-55902800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:55879400-55914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:55879600-55884600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:55879600-55891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:55879800-55884400	Strong transcription	HUVEC	blood vessel
50	chr2:55880000-55887800	Weak transcription	Duodenum Mucosa	Duodenum

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