Variant report

Variant	rs10408496
Chromosome Location	chr19:21351127-21351128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10401931	0.81[JPT][hapmap]
rs10406253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10406661	0.81[JPT][hapmap]
rs10407190	0.97[ASN][1000 genomes]
rs10409877	0.86[JPT][hapmap]
rs10410901	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs10412267	0.81[JPT][hapmap]
rs10423541	0.81[JPT][hapmap]
rs10854042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11085431	0.81[JPT][hapmap]
rs11668640	0.96[ASN][1000 genomes]
rs11672727	0.80[JPT][hapmap]
rs11672747	0.81[JPT][hapmap]
rs12608652	0.93[JPT][hapmap]
rs12980860	0.96[ASN][1000 genomes]
rs1470021	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs1609441	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs1864208	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1968523	0.81[JPT][hapmap]
rs1975056	0.91[ASN][1000 genomes]
rs2115493	0.81[JPT][hapmap]
rs2115494	0.81[JPT][hapmap]
rs2115495	0.81[JPT][hapmap]
rs2115498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2195453	0.81[JPT][hapmap]
rs2195454	0.81[JPT][hapmap]
rs2358806	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2358807	0.99[ASN][1000 genomes]
rs2358808	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs250002	0.83[EUR][1000 genomes]
rs250003	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2884554	0.80[JPT][hapmap]
rs2884555	0.81[ASN][1000 genomes]
rs29703	0.96[EUR][1000 genomes]
rs29705	0.96[EUR][1000 genomes]
rs29715	0.96[EUR][1000 genomes]
rs29720	0.96[EUR][1000 genomes]
rs29722	0.96[EUR][1000 genomes]
rs29729	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs30109	0.83[EUR][1000 genomes]
rs30111	0.83[EUR][1000 genomes]
rs388229	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324267	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs4488591	0.81[JPT][hapmap]
rs4809122	0.81[JPT][hapmap]
rs57740	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs606174	0.83[EUR][1000 genomes]
rs606958	0.83[EUR][1000 genomes]
rs6511188	0.81[JPT][hapmap]
rs6511191	0.81[JPT][hapmap]
rs6511192	0.81[JPT][hapmap]
rs6511195	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs6511202	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6511204	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6511205	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6511206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs694208	0.83[EUR][1000 genomes]
rs70950324	0.86[ASN][1000 genomes]
rs7246723	0.80[JPT][hapmap]
rs7249283	0.81[JPT][hapmap]
rs7249736	0.81[JPT][hapmap]
rs7250987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7254047	0.81[JPT][hapmap]
rs7254053	0.80[JPT][hapmap]
rs7254094	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs7256576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7258575	0.86[CHD][hapmap];0.93[JPT][hapmap]
rs7260268	0.80[JPT][hapmap]
rs7260600	0.81[JPT][hapmap]
rs72620580	0.90[EUR][1000 genomes]
rs72620581	0.90[EUR][1000 genomes]
rs8101918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8106801	1.00[CEU][hapmap]
rs8106923	0.81[JPT][hapmap]
rs8107638	0.81[JPT][hapmap]
rs8110848	0.87[ASN][1000 genomes]
rs8111827	0.81[JPT][hapmap]
rs8112054	0.81[JPT][hapmap]
rs8112216	0.81[JPT][hapmap]
rs8113541	0.81[JPT][hapmap]
rs9304980	0.81[JPT][hapmap]
rs9304982	0.86[JPT][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	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21325400-21361800	Weak transcription	Small Intestine	intestine
2	chr19:21325600-21365800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:21326000-21352600	Weak transcription	Right Ventricle	heart
4	chr19:21326000-21361000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:21326800-21361800	Weak transcription	Stomach Mucosa	stomach
6	chr19:21331000-21371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:21332800-21356400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:21333000-21373000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:21333200-21357400	Weak transcription	Pancreas	Pancrea
10	chr19:21333400-21364800	Weak transcription	HUVEC	blood vessel
11	chr19:21334600-21360800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:21335000-21365000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:21335800-21357000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:21335800-21362800	Weak transcription	Psoas Muscle	Psoas
15	chr19:21336000-21357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:21336000-21362000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr19:21336200-21351800	Weak transcription	Brain Anterior Caudate	brain
18	chr19:21336200-21352200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:21336200-21361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:21336200-21361800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:21336600-21360600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:21337000-21357000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:21338200-21354400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:21339200-21354200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:21339400-21361000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr19:21339400-21361000	Weak transcription	NHDF-Ad	bronchial
27	chr19:21340800-21352200	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:21341800-21361600	Weak transcription	Colon Smooth Muscle	Colon
29	chr19:21342000-21352200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:21342000-21355400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:21342000-21355400	Weak transcription	HMEC	breast
32	chr19:21342600-21351800	Weak transcription	NHLF	lung
33	chr19:21342800-21356800	Strong transcription	Dnd41	blood
34	chr19:21342800-21362600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:21343000-21352200	Weak transcription	A549	lung
36	chr19:21343400-21352600	Weak transcription	NH-A	brain
37	chr19:21343400-21358600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:21343600-21355200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr19:21343600-21359800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:21343800-21356400	Weak transcription	Aorta	Aorta
41	chr19:21344200-21359000	Strong transcription	Primary B cells from cord blood	blood
42	chr19:21345200-21351200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:21345400-21356400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:21345400-21357800	Weak transcription	Fetal Brain Male	brain
45	chr19:21345400-21358600	Weak transcription	Colonic Mucosa	Colon
46	chr19:21345400-21359200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:21345400-21361400	Weak transcription	Spleen	Spleen
48	chr19:21345600-21363000	Weak transcription	HepG2	liver
49	chr19:21345800-21353200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:21346400-21351800	Weak transcription	Brain Germinal Matrix	brain

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