Variant report

Variant	rs11264361
Chromosome Location	chr1:155289545-155289546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155289045-155291721	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:155289280-155289972	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:155289217-155291291	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:155285762-155295040	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:155288287-155291476	U87	brain:	n/a	n/a
6	POLR2A	chr1:155285992-155291727	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:155287588-155292287	HL-60	blood:	n/a	n/a
8	POLR2A	chr1:155287550-155292168	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr1:155289200-155289685	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:155286497-155292073	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr1:155287495-155292212	MCF-7	breast:	n/a	n/a
12	POLR2A	chr1:155289143-155289702	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:155289205-155289824	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:155287514-155291951	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:155289543-155291208	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr1:155288390-155289607	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:155289354-155289936	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:155289357-155291175	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr1:155289303-155289690	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:155285720-155292259	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr1:155287685-155291891	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:155289172-155292119	K562	blood:	n/a	n/a
23	POLR2A	chr1:155289491-155290164	ProgFib	skin:	n/a	n/a
24	POLR2A	chr1:155288607-155291751	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr1:155289133-155292282	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr1:155288293-155291535	U87	brain:	n/a	n/a
27	POLR2A	chr1:155289140-155289607	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr1:155289442-155289799	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:155288780-155290947	PBDE	blood:	n/a	n/a
30	POLR2A	chr1:155286517-155292132	K562	blood:	n/a	n/a
31	POLR2A	chr1:155288646-155291237	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:155286610-155292157	K562	blood:	n/a	n/a
33	POLR2A	chr1:155287248-155291990	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr1:155289332-155289643	HCT-116	colon:	n/a	n/a
35	POLR2A	chr1:155289426-155289795	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:155288984-155291335	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr1:155289042-155291565	K562	blood:	n/a	n/a
38	POLR2A	chr1:155286649-155291520	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:155175235..155178055-chr1:155287836..155290793,2	MCF-7	breast:
2	chr1:155226986..155228712-chr1:155289329..155291450,2	K562	blood:
3	chr1:155213696..155217007-chr1:155289069..155291862,3	K562	blood:
4	chr1:155218456..155235751-chr1:155288837..155299195,44	MCF-7	breast:
5	chr1:155239314..155245036-chr1:155288379..155297041,21	MCF-7	breast:
6	chr1:155231157..155233872-chr1:155289047..155290722,2	K562	blood:
7	chr1:155223299..155226083-chr1:155288003..155289831,2	MCF-7	breast:

No data

Variant related genes	Relation type
RUSC1	TF binding region
ENSG00000160767	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000177628	Chromatin interaction
ENSG00000116521	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1052176	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1052177	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10796941	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796943	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap]
rs10796945	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs10908461	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908462	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908465	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10908469	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11264349	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11264355	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11264357	0.83[EUR][1000 genomes]
rs11264358	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11264359	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264360	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11264363	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs11264367	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11264369	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11264371	1.00[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs11264372	1.00[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs11264375	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs12026638	0.95[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs12032720	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041534	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs12044063	0.84[EUR][1000 genomes]
rs12067675	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12079134	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12239114	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs12724079	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs12724449	0.82[EUR][1000 genomes]
rs12749306	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1325908	1.00[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap]
rs1360554	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1886905	0.84[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs2071053	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2297480	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3020781	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3814318	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4620533	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4971072	0.83[ASN][1000 genomes]
rs5005770	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs6672284	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6677385	0.81[EUR][1000 genomes]
rs6684889	0.89[CHB][hapmap]
rs6688636	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7524950	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7534795	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7554780	0.81[EUR][1000 genomes]
rs7556102	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs8177968	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8847	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs932972	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
2	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers 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	452 gene(s)	inside rSNPs	diseases
3	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
4	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
8	nsv946413	chr1:155286949-155296660	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11264361	DCST1	cis	parietal	SCAN
rs11264361	GBAP1	cis	Artery Tibial	GTEx
rs11264361	RIT1	cis	cerebellum	SCAN
rs11264361	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs11264361	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs11264361	THEM5	cis	parietal	SCAN
rs11264361	GBA	cis	Esophagus Mucosa	GTEx
rs11264361	FDPS	cis	lymphoblastoid	seeQTL
rs11264361	YY1AP1	cis	cerebellum	SCAN
rs11264361	GBAP1	cis	parietal	SCAN
rs11264361	SPRR2A	cis	cerebellum	SCAN
rs11264361	SPRR2D	cis	parietal	SCAN
rs11264361	PKLR	cis	Nerve Tibial	GTEx
rs11264361	LCE1C	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155279200-155290400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155279800-155290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155280000-155290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:155280000-155290200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:155280000-155290200	Weak transcription	Right Atrium	heart
6	chr1:155280000-155290400	Weak transcription	Psoas Muscle	Psoas
7	chr1:155280200-155289800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr1:155280200-155289800	Strong transcription	Fetal Stomach	stomach
9	chr1:155280200-155290000	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:155280600-155289800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:155280600-155289800	Weak transcription	Fetal Brain Male	brain
14	chr1:155280600-155290200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:155280600-155290200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:155280800-155290000	Strong transcription	Fetal Thymus	thymus
17	chr1:155280800-155290600	Weak transcription	Small Intestine	intestine
18	chr1:155281400-155290600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:155281600-155290200	Weak transcription	Stomach Mucosa	stomach
20	chr1:155281600-155290600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:155281800-155290000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:155282000-155289600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:155282200-155289800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:155282200-155290200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:155282200-155290600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:155282800-155289800	Strong transcription	Fetal Brain Female	brain
27	chr1:155283400-155290200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:155283600-155289800	Weak transcription	Fetal Heart	heart
29	chr1:155283600-155289800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:155283600-155290000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:155283600-155290000	Strong transcription	HSMMtube	muscle
32	chr1:155283600-155290400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:155284600-155290200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:155285000-155289800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:155285000-155289800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:155285000-155290000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:155285000-155290200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:155285000-155290200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:155285000-155290200	Weak transcription	Aorta	Aorta
40	chr1:155286000-155289600	Strong transcription	HSMM	muscle
41	chr1:155286000-155290000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:155286000-155290000	Strong transcription	NHEK	skin
43	chr1:155286000-155290200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:155286200-155289600	Strong transcription	Thymus	Thymus
45	chr1:155286200-155290800	Strong transcription	Dnd41	blood
46	chr1:155286600-155289600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:155286600-155290000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:155286600-155290000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:155286600-155290000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:155286600-155290200	Strong transcription	H9 Cell Line	embryonic stem cell

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