Variant report

Variant	rs35673421
Chromosome Location	chr3:49139406-49139407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49139378-49139556	K562	blood:	n/a	n/a
2	POLR2A	chr3:49139377-49139766	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49043447..49045313-chr3:49137618..49140002,2	K562	blood:
2	chr3:49058000..49061504-chr3:49138702..49143374,6	K562	blood:
3	chr3:49063558..49068659-chr3:49135988..49142189,8	MCF-7	breast:
4	chr3:49137934..49140259-chr3:49140747..49142873,2	MCF-7	breast:
5	chr3:49049216..49051915-chr3:49137148..49139973,2	MCF-7	breast:
6	chr3:49137640..49139439-chr3:49147793..49150282,2	K562	blood:
7	chr3:49058895..49061376-chr3:49135583..49140082,4	MCF-7	breast:

No data

Variant related genes	Relation type
QARS	TF binding region
ENSG00000172053	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000172046	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10154895	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs1134591	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710247	0.91[EUR][1000 genomes]
rs11712006	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11716334	0.82[ASN][1000 genomes]
rs11716614	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs11718982	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11719457	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11720460	0.89[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.80[ASN][1000 genomes]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12493001	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12636030	0.89[ASN][1000 genomes]
rs12637037	0.80[ASN][1000 genomes]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12715434	0.89[EUR][1000 genomes]
rs13064784	0.95[ASN][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs13072554	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs13080725	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13087930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs13090839	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13092715	1.00[JPT][hapmap]
rs13096406	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13315711	1.00[JPT][hapmap]
rs2117938	1.00[JPT][hapmap]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3212	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34326553	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343820	0.84[EUR][1000 genomes]
rs34504524	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34509487	0.83[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784192	0.89[EUR][1000 genomes]
rs34889065	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060561	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs35102816	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35108630	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.89[EUR][1000 genomes]
rs35283189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923475	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4308307	0.82[ASN][1000 genomes]
rs4364202	0.93[ASN][1000 genomes]
rs4499638	0.87[ASN][1000 genomes]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4536858	0.87[ASN][1000 genomes]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4955418	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4955432	1.00[JPT][hapmap]
rs4974078	0.87[CHD][hapmap]
rs4974080	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4974082	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5030795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55713230	0.87[ASN][1000 genomes]
rs55921200	0.85[AMR][1000 genomes]
rs56004653	0.81[AMR][1000 genomes]
rs56306491	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56318350	0.83[EUR][1000 genomes]
rs61583136	0.85[ASN][1000 genomes]
rs61729488	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62262517	0.93[ASN][1000 genomes]
rs6414613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6446196	1.00[CHB][hapmap]
rs6446205	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66991555	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67286839	0.89[EUR][1000 genomes]
rs6770112	0.85[ASN][1000 genomes]
rs6779394	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6781790	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.84[EUR][1000 genomes]
rs6784111	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6790914	0.87[ASN][1000 genomes]
rs6794924	0.82[ASN][1000 genomes]
rs6795025	0.87[ASN][1000 genomes]
rs71324929	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71324939	0.89[EUR][1000 genomes]
rs73082362	0.81[AMR][1000 genomes]
rs73084135	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7430198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7432989	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7615235	0.87[ASN][1000 genomes]
rs7621015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7628719	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7643368	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9637481	1.00[JPT][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9826525	0.89[EUR][1000 genomes]
rs9828310	0.89[EUR][1000 genomes]
rs9835439	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840050	1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs9846123	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9847839	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9850134	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9855123	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862483	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880088	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9884022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9990153	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs35673421	ALAS1	cis	cerebellum	SCAN
rs35673421	WDR6	cis	Esophagus Mucosa	GTEx
rs35673421	HEMK1	cis	parietal	SCAN
rs35673421	WDR6	cis	parietal	SCAN
rs35673421	KBTBD3	trans	parietal	SCAN
rs35673421	WDR6	cis	cerebellum	SCAN
rs35673421	NICN1	cis	cerebellum	SCAN
rs35673421	USP4	Cis_1M	lymphoblastoid	RTeQTL
rs35673421	RNF123	cis	parietal	SCAN
rs35673421	CSPG5	cis	parietal	SCAN
rs35673421	CCDC71	cis	cerebellum	SCAN
rs35673421	WDR6	cis	Adipose Subcutaneous	GTEx
rs35673421	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs35673421	WDR6	cis	Artery Tibial	GTEx
rs35673421	LRRC2	cis	cerebellum	SCAN
rs35673421	C3orf62	cis	cerebellum	SCAN
rs35673421	CCDC36	cis	cerebellum	SCAN
rs35673421	ARIH2	cis	cerebellum	SCAN
rs35673421	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49132400-49140800	Weak transcription	Right Atrium	heart
2	chr3:49132400-49141600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49133000-49140000	Strong transcription	HSMMtube	muscle
4	chr3:49133000-49140200	Strong transcription	NHLF	lung
5	chr3:49133000-49140400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:49133000-49140400	Strong transcription	Right Ventricle	heart
7	chr3:49133000-49140600	Strong transcription	Fetal Muscle Leg	muscle
8	chr3:49133000-49140600	Strong transcription	Osteobl	bone
9	chr3:49133000-49140800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:49133000-49140800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:49133000-49140800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:49133000-49140800	Strong transcription	Fetal Intestine Small	intestine
13	chr3:49133000-49140800	Strong transcription	Fetal Muscle Trunk	muscle
14	chr3:49133000-49140800	Strong transcription	Placenta	Placenta
15	chr3:49133000-49140800	Strong transcription	Fetal Stomach	stomach
16	chr3:49133200-49140000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:49133200-49140000	Strong transcription	Liver	Liver
18	chr3:49133200-49140200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:49133200-49140200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:49133200-49140200	Strong transcription	Adipose Nuclei	Adipose
21	chr3:49133200-49140200	Strong transcription	Lung	lung
22	chr3:49133200-49140400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:49133200-49140600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:49133200-49140600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:49133200-49140600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:49133200-49140600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:49133200-49140600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:49133200-49140600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr3:49133200-49140600	Strong transcription	Fetal Intestine Large	intestine
30	chr3:49133200-49140600	Strong transcription	Fetal Thymus	thymus
31	chr3:49133200-49140600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:49133200-49140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:49133200-49140800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:49133200-49140800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:49133200-49140800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:49133200-49141000	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr3:49133200-49141000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:49133200-49141000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:49133200-49141000	Strong transcription	Brain Cingulate Gyrus	brain
40	chr3:49133200-49141200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:49133400-49140200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:49133400-49140400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:49133400-49140600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:49133400-49140600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:49133400-49140600	Strong transcription	NHEK	skin
46	chr3:49133400-49140800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:49133400-49140800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:49133400-49140800	Strong transcription	Brain Germinal Matrix	brain
49	chr3:49133400-49141000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:49133600-49139600	Strong transcription	Hela-S3	cervix

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