Variant report

Variant	rs10732635
Chromosome Location	chr1:114519351-114519352
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr1:114518663-114520011	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:114518336-114522222	K562	blood:	n/a	n/a
3	TEAD4	chr1:114519141-114519994	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:114519235-114519368	ProgFib	skin:	n/a	n/a
5	ESR1	chr1:114519103-114519683	T-47D	breast:	n/a	chr1:114519402-114519417
6	ESR1	chr1:114519154-114519582	ECC-1	luminal epithelium:	n/a	chr1:114519402-114519417
7	GATA3	chr1:114519102-114519632	MCF-7	breast:	n/a	n/a
8	ESR1	chr1:114519093-114519573	T-47D	breast:	n/a	chr1:114519402-114519417
9	CEBPB	chr1:114519100-114519962	MCF-7	breast:	n/a	n/a
10	ESR1	chr1:114519062-114519944	ECC-1	luminal epithelium:	n/a	chr1:114519402-114519417
11	ESR1	chr1:114519085-114519678	T-47D	breast:	n/a	chr1:114519402-114519417
12	TEAD4	chr1:114519254-114519860	ECC-1	luminal epithelium:	n/a	n/a
13	ESR1	chr1:114519108-114519655	T-47D	breast:	n/a	chr1:114519402-114519417
14	CTCF	chr1:114519320-114519470	WI-38	lung:	n/a	n/a
15	ESR1	chr1:114519022-114519944	ECC-1	luminal epithelium:	n/a	chr1:114519402-114519417
16	POLR2A	chr1:114519319-114519444	K562	blood:	n/a	n/a
17	ZNF217	chr1:114519086-114519806	MCF-7	breast:	n/a	n/a
18	NFIC	chr1:114519215-114519920	ECC-1	luminal epithelium:	n/a	n/a
19	RAD21	chr1:114519277-114519883	H1-hESC	embryonic stem cell:	n/a	n/a
20	TCF12	chr1:114519047-114520024	ECC-1	luminal epithelium:	n/a	n/a
21	ESR1	chr1:114519089-114519808	ECC-1	luminal epithelium:	n/a	chr1:114519402-114519417
22	CTCF	chr1:114519240-114519390	GM12878	blood:	n/a	n/a
23	CTCF	chr1:114519280-114519430	HEK293	kidney:	n/a	n/a
24	EP300	chr1:114519034-114519957	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr1:114519280-114519430	HPF	lung:	n/a	n/a
26	TCF12	chr1:114519163-114519988	ECC-1	luminal epithelium:	n/a	n/a
27	ESR1	chr1:114519214-114519816	ECC-1	luminal epithelium:	n/a	chr1:114519402-114519417
28	CTCF	chr1:114519287-114519862	H1-hESC	embryonic stem cell:	n/a	n/a
29	HDAC2	chr1:114519195-114519909	MCF-7	breast:	n/a	n/a
30	POLR2A	chr1:114519169-114519619	HL-60	blood:	n/a	n/a
31	ESR1	chr1:114519030-114519883	ECC-1	luminal epithelium:	n/a	chr1:114519402-114519417
32	NR2F2	chr1:114518904-114520073	MCF-7	breast:	n/a	n/a
33	ESR1	chr1:114519176-114519602	T-47D	breast:	n/a	chr1:114519402-114519417
34	POLR2A	chr1:114519062-114519947	HL-60	blood:	n/a	n/a
35	POLR2A	chr1:114519282-114519696	Hela-S3	cervix:	n/a	n/a
36	ESR1	chr1:114519048-114519705	T-47D	breast:	n/a	chr1:114519402-114519417
37	RAD21	chr1:114519174-114519912	MCF-7	breast:	n/a	n/a
38	HA-E2F1	chr1:114519246-114519730	MCF-7	breast:	n/a	n/a
39	CTCF	chr1:114519247-114520073	MCF-7	breast:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114519008..114519800-chr1:115498966..115499533,2	MCF-7	breast:
2	chr1:114519068..114519924-chr1:114888867..114889460,3	MCF-7	breast:
3	chr1:114506613..114508905-chr1:114518738..114521439,2	MCF-7	breast:
4	chr1:114470804..114474068-chr1:114515316..114519565,7	MCF-7	breast:
5	chr1:114512401..114515204-chr1:114516877..114520311,4	K562	blood:
6	chr1:114517866..114521234-chr1:114758267..114762290,4	MCF-7	breast:
7	chr1:114519045..114519788-chr1:114576300..114577157,2	MCF-7	breast:
8	chr1:114518885..114519547-chr17:58142705..58143321,2	MCF-7	breast:
9	chr1:114518794..114519741-chr3:4356513..4357049,2	MCF-7	breast:
10	chr1:114518409..114520155-chr1:114764536..114766129,2	MCF-7	breast:
11	chr1:114518951..114519800-chr1:114576379..114577180,4	MCF-7	breast:
12	chr1:114353779..114355494-chr1:114518175..114520933,2	MCF-7	breast:
13	chr1:114519302..114519928-chr1:114825479..114826241,2	MCF-7	breast:
14	chr1:114519027..114521459-chr1:114540570..114543395,2	MCF-7	breast:
15	chr1:114519264..114519893-chr1:114761796..114762682,2	MCF-7	breast:
16	chr1:114519332..114519854-chr1:114542844..114543351,2	MCF-7	breast:
17	chr1:114518981..114519568-chr1:114543160..114543707,2	MCF-7	breast:
18	chr1:114519332..114519854-chr1:114542844..114543693,3	MCF-7	breast:
19	chr1:114519300..114519841-chr1:114585412..114586240,2	MCF-7	breast:

No data

Variant related genes	Relation type
OLFML3	TF binding region
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000163349	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10858024	0.83[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11811771	0.83[ASN][1000 genomes]
rs2358996	0.94[ASW][hapmap];0.89[CEU][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3789614	0.89[GIH][hapmap]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10732635	CASQ2	cis	cerebellum	SCAN
rs10732635	KCNC4	cis	parietal	SCAN
rs10732635	PTPN22	cis	parietal	SCAN
rs10732635	DCLRE1B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114496400-114519400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:114504800-114519400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:114511200-114521800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:114512200-114521000	Weak transcription	Fetal Heart	heart
5	chr1:114512800-114521600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:114513200-114521800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:114515000-114521600	Weak transcription	Fetal Brain Male	brain
8	chr1:114516000-114521600	Weak transcription	HMEC	breast
9	chr1:114516200-114521600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:114516200-114521600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:114516200-114521600	Weak transcription	Pancreas	Pancrea
12	chr1:114516200-114521600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:114516200-114521600	Weak transcription	NHEK	skin
14	chr1:114516200-114521800	Weak transcription	Gastric	stomach
15	chr1:114516200-114522000	Weak transcription	Right Ventricle	heart
16	chr1:114516200-114524600	Weak transcription	Small Intestine	intestine
17	chr1:114516400-114519400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:114516400-114521200	Weak transcription	HepG2	liver
19	chr1:114516400-114521600	Weak transcription	Aorta	Aorta
20	chr1:114517400-114519600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:114517400-114521600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:114517400-114521600	Weak transcription	Colonic Mucosa	Colon
23	chr1:114517400-114521600	Enhancers	HSMMtube	muscle
24	chr1:114517400-114522400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr1:114517400-114522400	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:114517600-114519400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr1:114517600-114519600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:114517600-114519600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr1:114517600-114519600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr1:114517600-114519600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:114517600-114519800	Genic enhancers	Fetal Thymus	thymus
32	chr1:114517600-114520000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:114517600-114520000	Enhancers	Adipose Nuclei	Adipose
34	chr1:114517600-114520200	Enhancers	NHLF	lung
35	chr1:114517600-114521200	Genic enhancers	Primary T cells from cord blood	blood
36	chr1:114517600-114521400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr1:114517600-114521400	Enhancers	Osteobl	bone
38	chr1:114517600-114521600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:114517600-114521600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:114517600-114521600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:114517600-114523400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:114517800-114519400	Weak transcription	Brain Angular Gyrus	brain
43	chr1:114517800-114519400	Genic enhancers	HUVEC	blood vessel
44	chr1:114517800-114519800	Enhancers	Psoas Muscle	Psoas
45	chr1:114517800-114520200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:114517800-114521600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:114518000-114519400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr1:114518000-114519600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:114518000-114519600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:114518000-114519800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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