Variant report

Variant	rs6511204
Chromosome Location	chr19:21340622-21340623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10406253	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10407190	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10408496	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10854042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11668640	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671623	1.00[YRI][hapmap]
rs12608652	0.94[JPT][hapmap];0.96[YRI][hapmap]
rs12980860	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16997503	0.95[CEU][hapmap];0.96[TSI][hapmap]
rs17445374	0.95[CEU][hapmap];0.92[TSI][hapmap]
rs17445381	0.95[CEU][hapmap]
rs1864208	0.95[ASN][1000 genomes]
rs1975056	0.91[ASN][1000 genomes]
rs2115498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2358806	0.98[ASN][1000 genomes]
rs2358807	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884555	0.82[ASN][1000 genomes]
rs29728	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs416001	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4324267	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs6511202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6511205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6511206	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs70950324	0.84[ASN][1000 genomes]
rs7248419	0.83[EUR][1000 genomes]
rs7250691	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7250987	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7251158	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7251646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7254094	0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.81[MKK][hapmap]
rs7256576	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7258575	0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs8101918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110848	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv1065384	chr19:21249321-21350698	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv911413	chr19:21263518-21347598	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6511204	ZNF429,LOC400680	cis	brain	BrainEAC
rs6511204	ZNF714	cis	cerebellum	SCAN
rs6511204	ZNF100	cis	cerebellum	SCAN
rs6511204	ZNF429	cis	cerebellum	SCAN
rs6511204	ZNF738	cis	parietal	SCAN
rs6511204	DDA1	cis	cerebellum	SCAN
rs6511204	ZNF714	cis	parietal	SCAN
rs6511204	RFXANK	cis	cerebellum	SCAN

Chromatin state (count:104 , 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	chr19:21327000-21342800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:21327000-21347000	Weak transcription	Hela-S3	cervix
8	chr19:21331000-21371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:21332200-21341400	Weak transcription	Osteobl	bone
10	chr19:21332800-21356400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:21333000-21350000	Weak transcription	Fetal Kidney	kidney
12	chr19:21333000-21373000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:21333200-21341600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:21333200-21347000	Weak transcription	Gastric	stomach
15	chr19:21333200-21357400	Weak transcription	Pancreas	Pancrea
16	chr19:21333400-21364800	Weak transcription	HUVEC	blood vessel
17	chr19:21334000-21344400	Weak transcription	Spleen	Spleen
18	chr19:21334600-21360800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:21335000-21365000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:21335800-21343000	Weak transcription	NH-A	brain
21	chr19:21335800-21348200	Weak transcription	Brain Substantia Nigra	brain
22	chr19:21335800-21357000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:21335800-21362800	Weak transcription	Psoas Muscle	Psoas
24	chr19:21336000-21341200	Weak transcription	Ovary	ovary
25	chr19:21336000-21341400	Weak transcription	HMEC	breast
26	chr19:21336000-21357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:21336000-21362000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:21336200-21341400	Weak transcription	NHEK	skin
29	chr19:21336200-21343000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr19:21336200-21344600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:21336200-21346000	Weak transcription	HSMMtube	muscle
32	chr19:21336200-21349800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:21336200-21349800	Weak transcription	Fetal Lung	lung
34	chr19:21336200-21350000	Weak transcription	Adipose Nuclei	Adipose
35	chr19:21336200-21350000	Weak transcription	Placenta	Placenta
36	chr19:21336200-21350400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:21336200-21351800	Weak transcription	Brain Anterior Caudate	brain
38	chr19:21336200-21352200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:21336200-21361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:21336200-21361800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr19:21336400-21341400	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:21336400-21342800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr19:21336400-21344000	Weak transcription	Primary B cells from peripheral blood	blood
44	chr19:21336400-21344400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:21336400-21349400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:21336600-21343000	Weak transcription	HSMM	muscle
47	chr19:21336600-21360600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:21336800-21345800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr19:21337000-21342800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr19:21337000-21357000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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