Variant report

Variant	rs9819511
Chromosome Location	chr3:49884261-49884262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49884022-49884285	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49883288..49885079-chr3:49939323..49941656,2	K562	blood:
2	chr3:49883594..49886564-chr3:49889140..49892041,2	K562	blood:
3	chr3:49882290..49886564-chr3:49889140..49892041,3	K562	blood:

Variant related genes	Relation type
TRAIP	TF binding region
ENSG00000164078	Chromatin interaction
ENSG00000228008	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10049413	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1049256	0.84[ASN][1000 genomes]
rs10865958	0.93[ASN][1000 genomes]
rs10865959	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130214	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130216	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130218	0.84[ASN][1000 genomes]
rs11130219	0.84[ASN][1000 genomes]
rs11130221	0.86[ASN][1000 genomes]
rs1128535	0.93[ASN][1000 genomes]
rs11709680	0.84[ASN][1000 genomes]
rs11710675	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11714957	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11715304	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11716575	0.84[ASN][1000 genomes]
rs11717256	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11717463	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11920900	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12381242	0.84[ASN][1000 genomes]
rs12490656	0.81[ASN][1000 genomes]
rs13063621	0.86[ASN][1000 genomes]
rs13084243	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13085679	0.93[ASN][1000 genomes]
rs13086130	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086465	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13090611	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1317140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13316065	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1491986	0.84[ASN][1000 genomes]
rs1799843	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1799845	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2234385	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2234391	0.90[ASN][1000 genomes]
rs2246832	0.95[ASN][1000 genomes]
rs2247036	0.95[ASN][1000 genomes]
rs2271960	0.95[ASN][1000 genomes]
rs2271961	0.95[ASN][1000 genomes]
rs2276864	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291542	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2307021	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2352967	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2352974	0.95[ASN][1000 genomes]
rs2352975	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34451146	0.86[ASN][1000 genomes]
rs34522271	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34614773	0.84[ASN][1000 genomes]
rs34735338	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35210174	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35261599	0.86[ASN][1000 genomes]
rs35474403	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749237	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749240	0.84[ASN][1000 genomes]
rs3749241	0.84[ASN][1000 genomes]
rs3811695	0.82[ASN][1000 genomes]
rs3811696	0.84[ASN][1000 genomes]
rs3819325	0.87[ASN][1000 genomes]
rs4519692	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855841	0.81[ASN][1000 genomes]
rs4855850	0.83[ASN][1000 genomes]
rs4855862	0.84[ASN][1000 genomes]
rs4855867	0.84[ASN][1000 genomes]
rs57648519	0.86[ASN][1000 genomes]
rs59906301	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60205400	0.86[ASN][1000 genomes]
rs62260715	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62260719	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62260729	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6446295	0.86[ASN][1000 genomes]
rs6766836	0.86[ASN][1000 genomes]
rs6775384	0.93[ASN][1000 genomes]
rs6785549	0.81[ASN][1000 genomes]
rs6802890	0.86[ASN][1000 genomes]
rs6804655	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs695238	0.93[ASN][1000 genomes]
rs71324996	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7431078	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431106	0.86[ASN][1000 genomes]
rs7618501	0.85[ASN][1000 genomes]
rs7618519	0.86[ASN][1000 genomes]
rs7629936	0.90[ASN][1000 genomes]
rs7634886	0.84[ASN][1000 genomes]
rs7634902	0.84[ASN][1000 genomes]
rs7645061	0.93[ASN][1000 genomes]
rs7648987	0.93[ASN][1000 genomes]
rs7649348	0.86[ASN][1000 genomes]
rs9814765	0.86[ASN][1000 genomes]
rs9815766	0.86[ASN][1000 genomes]
rs9850465	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9853458	0.84[ASN][1000 genomes]
rs9859153	0.86[ASN][1000 genomes]
rs9865480	0.84[ASN][1000 genomes]
rs9871654	0.85[ASN][1000 genomes]
rs9876508	0.86[ASN][1000 genomes]
rs9882639	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9819511	WDR6	cis	Whole Blood	GTEx
rs9819511	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49861200-49893200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:49864000-49893200	Weak transcription	Placenta	Placenta
3	chr3:49864200-49893000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:49864800-49886000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:49865000-49886000	Strong transcription	Dnd41	blood
6	chr3:49865600-49885800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:49865600-49885800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:49869400-49893000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:49870200-49893000	Weak transcription	HSMM	muscle
10	chr3:49871200-49886000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:49873600-49885800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:49873800-49885800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:49874000-49885800	Strong transcription	Thymus	Thymus
14	chr3:49877000-49893000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:49877000-49893400	Weak transcription	HSMMtube	muscle
16	chr3:49877200-49885000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:49877200-49886000	Weak transcription	Stomach Mucosa	stomach
18	chr3:49877200-49893000	Weak transcription	Gastric	stomach
19	chr3:49877200-49893000	Weak transcription	NHDF-Ad	bronchial
20	chr3:49877200-49893200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:49877400-49893000	Weak transcription	A549	lung
22	chr3:49877400-49893200	Weak transcription	Lung	lung
23	chr3:49877400-49893200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:49877600-49893200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:49877800-49885800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:49877800-49893000	Weak transcription	Esophagus	oesophagus
27	chr3:49877800-49893000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:49878000-49886000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:49878400-49885800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:49878800-49886000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:49879000-49885600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:49879000-49885800	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:49879000-49886000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:49879000-49893000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:49879000-49893000	Weak transcription	NHLF	lung
36	chr3:49879000-49893200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:49879200-49886000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:49879200-49886000	Strong transcription	Fetal Stomach	stomach
39	chr3:49879200-49893000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:49879200-49893000	Weak transcription	Hela-S3	cervix
41	chr3:49879400-49885600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:49879400-49885600	Strong transcription	Fetal Muscle Leg	muscle
43	chr3:49879400-49885800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:49879400-49885800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:49879400-49893000	Weak transcription	HUVEC	blood vessel
46	chr3:49879400-49893000	Weak transcription	NH-A	brain
47	chr3:49879600-49885600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr3:49879600-49886000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:49879800-49893000	Weak transcription	Fetal Brain Male	brain
50	chr3:49880000-49893000	Weak transcription	Fetal Brain Female	brain

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