Variant report

Variant	rs1910485
Chromosome Location	chr1:114490635-114490636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr1:114490445-114490758	K562	blood:	n/a	n/a
2	KAP1	chr1:114489235-114490664	HEK293	kidney:	n/a	n/a
3	IRF1	chr1:114490146-114490673	K562	blood:	n/a	chr1:114490489-114490502 chr1:114490486-114490500 chr1:114490486-114490503 chr1:114490489-114490500 chr1:114490490-114490500 chr1:114490484-114490501 chr1:114490490-114490504

No.	Distal block	Cell Line	Cell type
1	chr1:114455126..114458709-chr1:114488876..114491433,3	K562	blood:
2	chr1:114488439..114491155-chr1:114492850..114497140,4	MCF-7	breast:
3	chr1:114469025..114474353-chr1:114487576..114493379,11	K562	blood:
4	chr1:114353138..114356692-chr1:114488797..114493614,4	MCF-7	breast:
5	chr1:114382638..114384845-chr1:114488214..114490819,2	MCF-7	breast:
6	chr1:114489425..114491820-chr1:114493391..114496113,3	K562	blood:
7	chr1:114480724..114483569-chr1:114488715..114491848,4	K562	blood:
8	chr1:114483759..114485680-chr1:114489982..114493578,3	K562	blood:
9	chr1:114470845..114474120-chr1:114489434..114493268,5	K562	blood:

Variant related genes	Relation type
HIPK1	TF binding region
ENSG00000235527	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000231128	Chromatin interaction

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

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

rs_ID	r²[population]
rs10108	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494162	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10494163	0.88[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11102703	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102706	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102707	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102708	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102709	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12060750	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12125546	0.89[ASN][1000 genomes]
rs12127377	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12129050	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1217444	0.91[ASN][1000 genomes]
rs1503832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553449	0.97[ASN][1000 genomes]
rs1553450	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17852555	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1985435	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1985436	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2358996	0.82[YRI][hapmap]
rs41302825	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537800	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674384	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7364	0.88[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs7519860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7545300	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7546851	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs756493	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs878129	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1910485	OVGP1	cis	cerebellum	SCAN
rs1910485	DCLRE1B	cis	lymphoblastoid	seeQTL
rs1910485	DCLRE1B	cis	multi-tissue	Pritchard
rs1910485	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs1910485	DCLRE1B	cis	normal skin	skin_eQTL
rs1910485	DENND2C	cis	cerebellum	SCAN
rs1910485	PTPN22	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114473600-114499200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:114479000-114517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:114484000-114510400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:114484000-114510400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:114484000-114511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:114484200-114497800	Weak transcription	NHDF-Ad	bronchial
7	chr1:114484200-114499400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:114484200-114499600	Weak transcription	HMEC	breast
9	chr1:114484200-114504800	Weak transcription	Esophagus	oesophagus
10	chr1:114484200-114505600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:114484400-114510400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:114484600-114496400	Weak transcription	NHEK	skin
13	chr1:114485000-114491800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr1:114485000-114496400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:114485000-114500600	Weak transcription	Lung	lung
16	chr1:114485000-114510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:114486400-114497200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:114486400-114499800	Weak transcription	Fetal Brain Male	brain
19	chr1:114486600-114496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:114486600-114496400	Weak transcription	Placenta	Placenta
21	chr1:114486600-114497400	Weak transcription	Fetal Kidney	kidney
22	chr1:114487600-114495400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:114487800-114491400	Weak transcription	Fetal Stomach	stomach
24	chr1:114487800-114492200	Enhancers	Liver	Liver
25	chr1:114487800-114498800	Weak transcription	Left Ventricle	heart
26	chr1:114487800-114499200	Weak transcription	Ovary	ovary
27	chr1:114488000-114496600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:114488200-114491000	Enhancers	Primary B cells from cord blood	blood
29	chr1:114488200-114491200	Enhancers	Fetal Intestine Small	intestine
30	chr1:114488200-114499000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:114488400-114491400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr1:114488400-114492600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:114488600-114491000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:114488600-114491000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:114488600-114491200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr1:114488600-114491600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:114488600-114492200	Enhancers	Fetal Lung	lung
38	chr1:114488800-114490800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:114488800-114490800	Enhancers	Brain Hippocampus Middle	brain
40	chr1:114488800-114491000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:114488800-114491000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr1:114488800-114491000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:114488800-114491400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr1:114488800-114491800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:114488800-114492000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:114488800-114492400	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:114489200-114491000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:114489200-114491000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:114489400-114491000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:114489400-114491000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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