Variant report

Variant	rs11585845
Chromosome Location	chr1:155944189-155944190
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155943892-155944306	K562	blood:	n/a	n/a
2	POLR2A	chr1:155943560-155949842	HL-60	blood:	n/a	n/a
3	CTCF	chr1:155944103-155944316	HepG2	liver:	n/a	n/a
4	CTCF	chr1:155944160-155944310	SAEC	small airway:	n/a	n/a
5	CTCF	chr1:155943978-155944284	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:155944000-155944270	GM12873	blood:	n/a	n/a
7	CTCF	chr1:155944100-155944250	HEK293	kidney:	n/a	n/a
8	CTCF	chr1:155944040-155944190	K562	blood:	n/a	n/a
9	RAD21	chr1:155944045-155944371	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:155944021-155944276	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:155944130-155944266	HUVEC	blood vessel:	n/a	n/a
12	CTCF	chr1:155944149-155944240	MCF-7	breast:	n/a	n/a
13	CTCF	chr1:155944080-155944230	HepG2	liver:	n/a	n/a
14	CTCF	chr1:155944060-155944210	GM12874	blood:	n/a	n/a
15	CTCF	chr1:155944160-155944310	HCT-116	colon:	n/a	n/a
16	PAX5	chr1:155944162-155944538	GM12878	blood:	n/a	chr1:155944371-155944389
17	POLR2A	chr1:155943832-155953868	U87	brain:	n/a	n/a
18	CTCF	chr1:155944140-155944290	HUVEC	blood vessel:	n/a	n/a
19	CTCF	chr1:155944060-155944210	HMEC	breast:	n/a	n/a
20	RAD21	chr1:155944060-155944301	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:155943838-155953803	U87	brain:	n/a	n/a
22	PAX5	chr1:155944038-155944600	GM12878	blood:	n/a	chr1:155944371-155944389
23	POLR2A	chr1:155944022-155944586	K562	blood:	n/a	n/a
24	POLR2A	chr1:155943861-155950165	GM12878	blood:	n/a	n/a
25	MTA3	chr1:155943968-155951505	GM12878	blood:	n/a	n/a
26	CTCF	chr1:155944160-155944310	WERI-Rb-1	eye:	n/a	n/a
27	CTCF	chr1:155944100-155944250	GM06990	blood:	n/a	n/a
28	STAT5A	chr1:155944168-155945223	GM12878	blood:	n/a	chr1:155944894-155944901 chr1:155944776-155944788 chr1:155944581-155944593 chr1:155944770-155944782
29	CTCF	chr1:155944142-155944250	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr1:155944140-155944290	HMEC	breast:	n/a	n/a
31	CTCF	chr1:155944100-155944250	HEEpiC	esophagus:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155943579..155945946-chr1:155950039..155953037,2	MCF-7	breast:
2	chr1:155942604..155944282-chr1:155975021..155977140,2	K562	blood:
3	chr1:155943593..155946344-chr1:155989264..155990773,2	K562	blood:

No data

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000273002	TF binding region
ENSG00000116584	Chromatin interaction
ENSG00000163479	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10796955	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1111102	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs11264426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037177	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs12080846	0.93[ASN][1000 genomes]
rs12091273	0.93[ASN][1000 genomes]
rs12091361	0.93[ASN][1000 genomes]
rs12118795	0.90[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12568523	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1889532	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1889533	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2016251	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.92[ASN][1000 genomes]
rs2282301	0.95[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2297649	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364403	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs4661175	0.93[ASW][hapmap]
rs4661217	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4661218	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61813286	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6427297	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs6667652	0.95[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs6670493	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6696019	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs729022	0.82[MEX][hapmap]
rs7534858	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867549	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs867550	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs915178	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs915181	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[ASN][1000 genomes]
rs928596	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11585845	RIT1	cis	Thyroid	GTEx
rs11585845	ROBLD3	cis	parietal	SCAN
rs11585845	SPRR3	cis	parietal	SCAN
rs11585845	PRUNE	cis	cerebellum	SCAN
rs11585845	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs11585845	YY1AP1	cis	cerebellum	SCAN
rs11585845	RIT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155934800-155944400	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr1:155935000-155944800	Enhancers	Fetal Heart	heart
4	chr1:155936600-155944200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:155936800-155944600	Genic enhancers	Fetal Stomach	stomach
6	chr1:155937000-155944200	Genic enhancers	Thymus	Thymus
7	chr1:155938000-155944400	Genic enhancers	Fetal Thymus	thymus
8	chr1:155940400-155944200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:155940400-155944400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:155940800-155944200	Enhancers	Fetal Lung	lung
11	chr1:155941000-155944200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:155941000-155944200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr1:155941000-155944800	Enhancers	HUVEC	blood vessel
14	chr1:155941000-155945000	Weak transcription	Pancreas	Pancrea
15	chr1:155941200-155944200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:155941600-155945000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:155941800-155944200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:155941800-155944200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:155941800-155944200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:155941800-155944400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:155941800-155944400	Genic enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:155941800-155944800	Genic enhancers	Dnd41	blood
23	chr1:155941800-155945200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:155941800-155945400	Enhancers	Psoas Muscle	Psoas
25	chr1:155942000-155944400	Genic enhancers	NHLF	lung
26	chr1:155942000-155944400	Weak transcription	Osteobl	bone
27	chr1:155942000-155944800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
28	chr1:155942200-155944200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:155942200-155944200	Enhancers	Brain Angular Gyrus	brain
30	chr1:155942400-155944200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:155942600-155944200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:155942600-155944200	Weak transcription	Small Intestine	intestine
33	chr1:155942800-155944400	Genic enhancers	NHDF-Ad	bronchial
34	chr1:155942800-155944600	Enhancers	Right Ventricle	heart
35	chr1:155942800-155945000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:155943000-155944200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:155943000-155944200	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr1:155943000-155944400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:155943000-155944400	Weak transcription	Aorta	Aorta
40	chr1:155943000-155944400	Genic enhancers	K562	blood
41	chr1:155943000-155945000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:155943000-155945400	Enhancers	Placenta	Placenta
43	chr1:155943000-155947400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:155943200-155944200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:155943200-155944200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:155943200-155944200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:155943200-155944200	Weak transcription	A549	lung
48	chr1:155943200-155944400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr1:155943200-155944600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:155943400-155944200	Enhancers	Muscle Satellite Cultured Cells	--

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