Variant report

Variant	rs274311
Chromosome Location	chr10:25244919-25244920
allele	A/G
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	STAT3	chr10:25244863-25244923	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr10:25244914-25245170	K562	blood:	n/a	n/a
3	FOS	chr10:25244680-25244954	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr10:25244680-25244940	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:25218576..25220907-chr10:25243610..25245926,2	K562	blood:
2	chr10:25244301..25246252-chr10:25263526..25265858,2	K562	blood:
3	chr10:25239628..25245194-chr10:25304841..25307327,7	K562	blood:

Variant related genes	Relation type
PRTFDC1	TF binding region
ENSG00000185875	Chromatin interaction
ENSG00000151023	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1000875	0.82[CHB][hapmap]
rs10508685	0.82[CHB][hapmap]
rs10508686	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs10741071	0.82[JPT][hapmap]
rs10741072	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10764515	0.84[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap]
rs10764518	0.82[CHB][hapmap]
rs10764519	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs10828728	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs10828731	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10828741	0.81[CHB][hapmap]
rs10828745	0.81[CHB][hapmap]
rs10828751	0.85[CEU][hapmap]
rs11014318	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11014320	0.85[ASN][1000 genomes]
rs11014357	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs12249889	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs12256642	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs12761282	0.87[ASN][1000 genomes]
rs12784769	0.86[CHB][hapmap]
rs1492608	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs1546097	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs185669	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap]
rs200730	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2031600	0.88[ASN][1000 genomes]
rs2035888	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2131276	0.82[CHB][hapmap]
rs2279547	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs2291583	0.91[CHD][hapmap]
rs2307047	0.86[CHD][hapmap]
rs2478091	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274288	0.90[ASN][1000 genomes]
rs274289	0.90[ASN][1000 genomes]
rs274290	0.82[ASN][1000 genomes]
rs274299	0.81[ASN][1000 genomes]
rs274301	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs274303	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274304	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs274306	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274307	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs274308	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274309	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274310	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs274312	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs274313	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs274316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2818289	0.87[ASN][1000 genomes]
rs3000491	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3748223	0.82[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs3808907	0.86[YRI][hapmap]
rs4345864	0.82[CHB][hapmap]
rs4748993	0.80[CEU][hapmap]
rs4748996	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs612482	0.81[ASN][1000 genomes]
rs6482467	0.82[CHB][hapmap]
rs6482468	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7086282	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs7393543	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs7913853	0.82[CHB][hapmap]
rs902904	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs902905	0.82[CHB][hapmap]
rs987274	0.81[CEU][hapmap];0.82[CHB][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	nsv1053278	chr10:25140776-25269093	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs274311	OTUD1	cis	parietal	SCAN
rs274311	THNSL1	cis	parietal	SCAN
rs274311	PIP4K2A	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25242200-25246400	Weak transcription	HSMM	muscle
2	chr10:25242200-25247800	Weak transcription	Aorta	Aorta
3	chr10:25242200-25247800	Weak transcription	Left Ventricle	heart
4	chr10:25242200-25248000	Weak transcription	Psoas Muscle	Psoas
5	chr10:25242400-25245600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:25242400-25246200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:25242400-25246600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:25242400-25246800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:25242400-25247400	Weak transcription	Ovary	ovary
10	chr10:25242400-25251400	Weak transcription	Liver	Liver
11	chr10:25242400-25252800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:25242600-25245800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:25242600-25245800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:25242600-25245800	Weak transcription	Osteobl	bone
15	chr10:25242600-25246800	Weak transcription	HUVEC	blood vessel
16	chr10:25242600-25247400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr10:25242600-25247600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:25242600-25249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr10:25242800-25245600	Weak transcription	Hela-S3	cervix
20	chr10:25242800-25245800	Weak transcription	Brain Angular Gyrus	brain
21	chr10:25242800-25246000	Weak transcription	NH-A	brain
22	chr10:25242800-25246600	Weak transcription	NHEK	skin
23	chr10:25242800-25247200	Weak transcription	Fetal Kidney	kidney
24	chr10:25242800-25247400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:25242800-25247600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:25242800-25247800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr10:25242800-25247800	Weak transcription	Right Atrium	heart
28	chr10:25242800-25251400	Weak transcription	Fetal Intestine Large	intestine
29	chr10:25242800-25251600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr10:25243000-25245600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:25243000-25245600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr10:25243000-25245600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:25243000-25245600	Weak transcription	HMEC	breast
34	chr10:25243000-25245800	Weak transcription	Brain Germinal Matrix	brain
35	chr10:25243000-25245800	Weak transcription	A549	lung
36	chr10:25243000-25246400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr10:25243000-25246400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr10:25243000-25246600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr10:25243000-25246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr10:25243000-25246800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:25243000-25246800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr10:25243000-25247000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr10:25243000-25247200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr10:25243000-25247200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr10:25243000-25247200	Weak transcription	Fetal Brain Female	brain
46	chr10:25243000-25247200	Weak transcription	Stomach Mucosa	stomach
47	chr10:25243000-25247600	Weak transcription	Fetal Brain Male	brain
48	chr10:25243000-25251400	Weak transcription	Fetal Intestine Small	intestine
49	chr10:25243200-25245400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:25243200-25245600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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