Variant report

Variant	rs4499638
Chromosome Location	chr3:49202782-49202783
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49202383-49203548	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:49202056-49203171	GM12891	blood:	n/a	n/a
3	POLR2A	chr3:49198510-49204140	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:49202709-49203409	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:49202210-49203969	K562	blood:	n/a	n/a
6	POLR2A	chr3:49202109-49202948	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:49202617-49202824	H1-hESC	embryonic stem cell:	n/a	n/a
8	WRNIP1	chr3:49202662-49202795	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49202346-49204220	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:49202635-49202927	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:49202505-49203058	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:49202328-49203080	HCT-116	colon:	n/a	n/a
13	POLR2A	chr3:49200938-49204840	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:49201097-49203519	GM12891	blood:	n/a	n/a
15	MTA3	chr3:49201975-49203510	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:49201051-49204100	K562	blood:	n/a	n/a
17	POLR2A	chr3:49201662-49203871	K562	blood:	n/a	n/a
18	POLR2A	chr3:49202157-49204071	GM12892	blood:	n/a	n/a
19	POLR2A	chr3:49202215-49204109	HL-60	blood:	n/a	n/a
20	POLR2A	chr3:49202499-49202788	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:49197955-49203552	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr3:49202632-49203012	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:49201981-49204035	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:49202073-49202936	GM12892	blood:	n/a	n/a
25	MXI1	chr3:49202262-49204871	IMR90	lung:	n/a	chr3:49204817-49204826
26	HEY1	chr3:49202620-49203212	K562	blood:	n/a	n/a
27	POLR2A	chr3:49202550-49204032	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr3:49202537-49203256	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:49201921-49203517	GM12878	blood:	n/a	n/a
30	TFAP2C	chr3:49202735-49204251	Hela-S3	cervix:	n/a	chr3:49203772-49203781
31	GTF2F1	chr3:49202705-49202859	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr3:49202522-49202884	HCT-116	colon:	n/a	n/a
33	HCFC1	chr3:49202399-49204676	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:49202052-49203366	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr3:49202652-49202789	MCF-7	breast:	n/a	n/a
36	POLR2A	chr3:49198512-49204161	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:49202128-49202837	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr3:49202570-49203920	IMR90	lung:	n/a	n/a
39	POLR2A	chr3:49202507-49202932	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:49202609-49203054	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49156700..49159998-chr3:49200731..49203876,4	MCF-7	breast:
2	chr3:49201275..49203674-chr3:49330511..49332743,2	K562	blood:
3	chr3:49056328..49059544-chr3:49202143..49205448,5	MCF-7	breast:
4	chr3:49202240..49204456-chr3:49315403..49317185,2	K562	blood:
5	chr3:49202004..49204374-chr8:125485548..125487898,2	MCF-7	breast:
6	chr3:49200574..49202840-chr3:49207823..49210788,2	MCF-7	breast:
7	chr3:49062283..49063958-chr3:49200924..49203151,2	MCF-7	breast:
8	chr3:49200663..49203264-chr3:49203598..49205710,2	MCF-7	breast:
9	chr3:49154967..49157191-chr3:49202240..49204149,2	MCF-7	breast:
10	chr3:49058597..49061483-chr3:49200742..49203028,2	K562	blood:
11	chr2:219260405..219263018-chr3:49201388..49203656,2	MCF-7	breast:
12	chr3:49140491..49143701-chr3:49201484..49205334,5	K562	blood:
13	chr3:49165625..49169555-chr3:49201131..49204246,4	MCF-7	breast:
14	chr3:49202213..49205140-chr3:49207105..49209971,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270441	TF binding region
ENSG00000144579	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000185909	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10154895	0.97[ASN][1000 genomes]
rs10865954	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130182	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130184	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130185	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11552724	0.87[ASN][1000 genomes]
rs11706189	0.97[ASN][1000 genomes]
rs11712006	0.87[ASN][1000 genomes]
rs11713297	0.97[ASN][1000 genomes]
rs11715581	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11716334	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11717524	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11719220	0.81[ASN][1000 genomes]
rs11920267	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12487580	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493001	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629637	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12629759	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12631989	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12636030	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637576	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13064780	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13064784	0.82[ASN][1000 genomes]
rs13096406	0.89[ASN][1000 genomes]
rs2117938	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2334958	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3212	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34326553	0.87[ASN][1000 genomes]
rs34580506	0.87[ASN][1000 genomes]
rs34889065	0.87[ASN][1000 genomes]
rs35174559	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35218722	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35283189	0.87[ASN][1000 genomes]
rs35673421	0.87[ASN][1000 genomes]
rs4279134	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4308307	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4364202	0.80[ASN][1000 genomes]
rs4367098	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4513485	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4521268	0.82[ASN][1000 genomes]
rs4536858	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955410	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955419	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955420	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955432	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5030795	0.87[ASN][1000 genomes]
rs55713230	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61583136	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62262517	0.80[ASN][1000 genomes]
rs66991555	0.87[ASN][1000 genomes]
rs6770112	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6779394	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784111	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6790914	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794924	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795756	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7626445	0.82[ASN][1000 genomes]
rs7638154	0.81[EUR][1000 genomes]
rs7645551	0.82[EUR][1000 genomes]
rs7652746	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9814987	0.92[ASN][1000 genomes]
rs9835439	0.92[ASN][1000 genomes]
rs9837237	0.95[ASN][1000 genomes]
rs9837625	0.95[ASN][1000 genomes]
rs9840050	0.82[ASN][1000 genomes]
rs9855123	0.92[ASN][1000 genomes]
rs9862483	0.97[ASN][1000 genomes]
rs9880088	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs4499638	NCKIPSD	cis	Esophagus Mucosa	GTEx
rs4499638	WDR6	cis	Esophagus Muscularis	GTEx
rs4499638	CCDC36	cis	Artery Tibial	GTEx
rs4499638	WDR6	cis	Esophagus Mucosa	GTEx
rs4499638	AMT	cis	Muscle Skeletal	GTEx
rs4499638	WDR6	cis	Heart Left Ventricle	GTEx
rs4499638	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4499638	CCDC36	cis	Esophagus Muscularis	GTEx
rs4499638	WDR6	cis	Adipose Subcutaneous	GTEx
rs4499638	AMT	cis	Thyroid	GTEx
rs4499638	ARIH2	cis	Thyroid	GTEx
rs4499638	WDR6	cis	Muscle Skeletal	GTEx
rs4499638	WDR6	cis	lung	GTEx
rs4499638	NICN1-AS1	cis	Thyroid	GTEx
rs4499638	WDR6	cis	Artery Tibial	GTEx
rs4499638	AMT	cis	Artery Aorta	GTEx
rs4499638	AMT	cis	Whole Blood	GTEx
rs4499638	NICN1	cis	Thyroid	GTEx
rs4499638	WDR6	cis	Whole Blood	GTEx
rs4499638	NCKIPSD	cis	Muscle Skeletal	GTEx
rs4499638	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4499638	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs4499638	WDR6	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49201200-49202800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr3:49201800-49202800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:49201800-49202800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:49202000-49202800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:49202000-49202800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:49202000-49202800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:49202000-49202800	Enhancers	Thymus	Thymus
8	chr3:49202000-49203200	Enhancers	Spleen	Spleen
9	chr3:49202000-49204400	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr3:49202200-49202800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:49202200-49202800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:49202200-49202800	Enhancers	Primary B cells from peripheral blood	blood
13	chr3:49202200-49202800	Enhancers	Fetal Brain Male	brain
14	chr3:49202200-49202800	Genic enhancers	Placenta	Placenta
15	chr3:49202200-49202800	Enhancers	Right Atrium	heart
16	chr3:49202200-49202800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr3:49202200-49202800	Flanking Active TSS	HepG2	liver
18	chr3:49202200-49203000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:49202200-49203000	Enhancers	Small Intestine	intestine
20	chr3:49202200-49203200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr3:49202200-49203400	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr3:49202200-49203400	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr3:49202200-49203400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:49202400-49202800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
25	chr3:49202400-49202800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:49202400-49202800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:49202400-49202800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr3:49202400-49202800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:49202400-49202800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:49202400-49202800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:49202400-49202800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:49202400-49202800	Enhancers	Esophagus	oesophagus
33	chr3:49202400-49202800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
34	chr3:49202400-49202800	Enhancers	Fetal Heart	heart
35	chr3:49202400-49202800	Flanking Active TSS	Lung	lung
36	chr3:49202400-49202800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
37	chr3:49202400-49202800	Flanking Active TSS	HMEC	breast
38	chr3:49202400-49202800	Flanking Active TSS	NHDF-Ad	bronchial
39	chr3:49202400-49202800	Transcr. at gene 5' and 3'	NHEK	skin
40	chr3:49202400-49203000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr3:49202400-49203000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr3:49202400-49203000	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr3:49202400-49203000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr3:49202400-49203000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr3:49202400-49203000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:49202400-49203000	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr3:49202400-49203000	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr3:49202400-49203000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr3:49202400-49203000	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr3:49202400-49203000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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