Variant report

Variant	rs11204668
Chromosome Location	chr1:150543686-150543687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr1:150543459-150544158	GM12878	blood:	n/a	n/a
2	FOS	chr1:150543654-150543826	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:150543194-150546558	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:150538698-150546656	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
6	POLR2A	chr1:150538866-150546573	U87	brain:	n/a	n/a
7	POLR2A	chr1:150539774-150546448	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:150543263-150543957	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr1:150541963-150546408	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr1:150543224-150546653	K562	blood:	n/a	n/a
11	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
12	SIN3AK20	chr1:150543601-150546543	K562	blood:	n/a	n/a
13	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
14	POLR2A	chr1:150543522-150543961	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr1:150543600-150543882	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:150540216-150546538	U87	brain:	n/a	n/a
17	POLR2A	chr1:150538654-150552953	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:150543506-150544212	SK-N-SH	brain:	n/a	n/a
19	BCLAF1	chr1:150543454-150544272	K562	blood:	n/a	chr1:150543944-150543953
20	POLR2A	chr1:150543314-150546680	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:150543535-150543911	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr1:150539727-150546572	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:150538736-150552926	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:150538866-150553173	U87	brain:	n/a	n/a
26	POLR2A	chr1:150538945-150546560	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr1:150542833-150544015	ECC-1	luminal epithelium:	n/a	n/a
28	TAF7	chr1:150543496-150544108	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:150542302-150546578	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr1:150543470-150543900	HCT-116	colon:	n/a	n/a
31	POLR2A	chr1:150538877-150553278	Hela-S3	cervix:	n/a	n/a
32	CHD2	chr1:150543679-150544181	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:150538822-150553196	H1-hESC	embryonic stem cell:	n/a	n/a
34	RCOR1	chr1:150543658-150543813	K562	blood:	n/a	n/a
35	POLR2A	chr1:150539636-150544211	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr1:150542706-150546537	K562	blood:	n/a	n/a
37	POLR2A	chr1:150543438-150546395	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:150542040-150546487	GM12891	blood:	n/a	n/a
39	POLR2A	chr1:150541942-150546679	GM12891	blood:	n/a	n/a
40	POLR2A	chr1:150543514-150544245	GM12891	blood:	n/a	n/a
41	POLR2A	chr1:150541930-150546677	GM12891	blood:	n/a	n/a
42	POLR2A	chr1:150543208-150546659	GM12891	blood:	n/a	n/a
43	POLR2A	chr1:150543593-150544175	GM19099	blood:	n/a	n/a
44	NR2F2	chr1:150543285-150544066	K562	blood:	n/a	n/a
45	POLR2A	chr1:150538740-150553070	K562	blood:	n/a	n/a
46	POLR2A	chr1:150538874-150549135	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:150543394-150546610	GM19193	blood:	n/a	n/a
48	POLR2A	chr1:150543574-150544186	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:150538937-150546714	GM12892	blood:	n/a	n/a
50	POLR2A	chr1:150543628-150544021	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150541344..150544160-chr1:150572544..150574410,2	K562	blood:
2	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
3	chr1:150543642..150545689-chr1:150586263..150588774,2	MCF-7	breast:
4	chr1:150542528..150547161-chr1:150576124..150579510,4	K562	blood:
5	chr1:150542533..150544635-chr1:150845972..150847579,2	MCF-7	breast:
6	chr1:150486114..150488258-chr1:150542189..150544516,3	K562	blood:
7	chr1:150542198..150544708-chr1:150893350..150895206,2	K562	blood:
8	chr1:150542997..150546031-chr1:150978720..150981188,4	MCF-7	breast:
9	chr1:150541549..150544184-chr1:150897269..150900025,2	K562	blood:
10	chr1:150542073..150543694-chr1:150971121..150973103,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL473P	TF binding region
RN7SL600P	TF binding region
ENSG00000143420	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000228126	Chromatin interaction
ENSG00000253047	Chromatin interaction
ENSG00000143379	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 31 )

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

rs_ID	r²[population]
rs1053732	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10888384	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10888385	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11204669	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11204675	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11204676	0.83[AFR][1000 genomes]
rs11204677	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204678	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11204679	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204680	0.89[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11204684	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11585169	1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12116492	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12125672	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126271	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12139563	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12406712	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12746899	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1971378	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2048558	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3738484	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738485	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754209	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4970918	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970923	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4971041	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55862611	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61820165	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6669122	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6697620	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6698495	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs878471	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932054	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9803935	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs11204668	POLR3GL	cis	cerebellum	SCAN
rs11204668	CTSS	cis	cerebellum	SCAN
rs11204668	FMO5	cis	cerebellum	SCAN
rs11204668	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204668	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204668	HORMAD1	cis	normal skin	skin_eQTL
rs11204668	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204668	CTSK	cis	lymphoblastoid	seeQTL
rs11204668	ARNT	cis	Thyroid	GTEx
rs11204668	CTSK	cis	cerebellum	SCAN
rs11204668	CTSK	cis	parietal	SCAN
rs11204668	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204668	C1orf54	cis	cerebellum	SCAN
rs11204668	TCHHL1	cis	parietal	SCAN
rs11204668	LCE4A	cis	cerebellum	SCAN
rs11204668	HORMAD1	cis	uninvolved skin	skin_eQTL
rs11204668	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204668	ARNT	cis	cerebellum	SCAN
rs11204668	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204668	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204668	PSMD4	cis	parietal	SCAN
rs11204668	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204668	ARNT	cis	normal skin	skin_eQTL
rs11204668	CTSS	cis	parietal	SCAN
rs11204668	GOLPH3L	cis	Nerve Tibial	GTEx
rs11204668	HORMAD1	cis	Nerve Tibial	GTEx
rs11204668	MCL1	cis	cerebellum	SCAN
rs11204668	ARNT	cis	parietal	SCAN
rs11204668	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11204668	ENSA	cis	cerebellum	SCAN
rs11204668	HORMAD1	cis	lesional skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150534400-150547200	Weak transcription	Ovary	ovary
2	chr1:150538800-150543800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr1:150538800-150543800	Enhancers	HMEC	breast
4	chr1:150540600-150544200	Enhancers	NHLF	lung
5	chr1:150540600-150544800	Enhancers	Psoas Muscle	Psoas
6	chr1:150540800-150543800	Enhancers	NHDF-Ad	bronchial
7	chr1:150540800-150545600	Enhancers	Right Atrium	heart
8	chr1:150540800-150545600	Enhancers	Right Ventricle	heart
9	chr1:150541400-150543800	Enhancers	NHEK	skin
10	chr1:150541400-150544200	Enhancers	Fetal Heart	heart
11	chr1:150541400-150545400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:150541400-150545600	Genic enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:150541400-150545800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:150541400-150547200	Genic enhancers	Fetal Intestine Small	intestine
15	chr1:150541400-150549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:150541600-150543800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:150541600-150543800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:150541600-150544000	Enhancers	Colon Smooth Muscle	Colon
19	chr1:150541600-150544400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:150541600-150545200	Weak transcription	Fetal Kidney	kidney
21	chr1:150541600-150545600	Weak transcription	Brain Angular Gyrus	brain
22	chr1:150541800-150544400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr1:150541800-150544600	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr1:150541800-150546800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:150542000-150544000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
26	chr1:150542000-150545400	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr1:150542000-150545600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:150542000-150545600	Strong transcription	Fetal Brain Female	brain
29	chr1:150542000-150547200	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:150542200-150544000	Enhancers	Aorta	Aorta
31	chr1:150542200-150545200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:150542200-150545600	Genic enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:150542200-150547200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:150542200-150547200	Strong transcription	Brain Germinal Matrix	brain
35	chr1:150542200-150548000	Genic enhancers	Placenta	Placenta
36	chr1:150542400-150543800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr1:150542400-150544000	Genic enhancers	Primary T cells from cord blood	blood
38	chr1:150542400-150544000	Genic enhancers	Fetal Thymus	thymus
39	chr1:150542400-150544400	Strong transcription	Fetal Intestine Large	intestine
40	chr1:150542400-150544800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:150542400-150545600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:150542400-150546800	Genic enhancers	Fetal Muscle Leg	muscle
43	chr1:150542400-150547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:150542600-150543800	Enhancers	Rectal Smooth Muscle	rectum
45	chr1:150542600-150544000	Genic enhancers	Duodenum Mucosa	Duodenum
46	chr1:150542600-150544200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr1:150542600-150545000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:150542600-150545200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:150542600-150545400	Weak transcription	Brain Substantia Nigra	brain
50	chr1:150542600-150545600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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