Variant report

Variant	rs10162550
Chromosome Location	chr14:39740406-39740407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39736982..39739247-chr14:39739513..39742286,3	K562	blood:
2	chr14:39639538..39641336-chr14:39738634..39740819,2	MCF-7	breast:
3	chr14:39737724..39741488-chr14:39742832..39745249,3	K562	blood:
4	chr14:39733456..39736427-chr14:39738159..39742075,4	K562	blood:
5	chr14:39733186..39738068-chr14:39738751..39742738,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258941	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000182400	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10131617	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10133417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10134143	0.87[ASN][1000 genomes]
rs10134365	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10137352	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10137905	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs10138024	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10138869	0.91[JPT][hapmap]
rs10151659	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10872920	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs11157053	0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs11157058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11620695	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11621264	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11621330	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11621822	0.88[ASN][1000 genomes]
rs11624839	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11626150	0.87[ASN][1000 genomes]
rs11626679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11627580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11628075	0.86[ASN][1000 genomes]
rs11845046	0.89[ASN][1000 genomes]
rs12434140	0.95[JPT][hapmap]
rs12587713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588386	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12588728	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12589831	0.88[ASN][1000 genomes]
rs12590172	0.80[JPT][hapmap]
rs12882709	0.88[ASN][1000 genomes]
rs12883781	0.80[ASN][1000 genomes]
rs12892482	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12894855	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs12894960	0.82[ASN][1000 genomes]
rs12896838	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1594842	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17109021	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17109028	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17109056	0.89[ASN][1000 genomes]
rs17109073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17109100	0.80[ASN][1000 genomes]
rs1897792	0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs1950952	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1998194	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2082635	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2274395	0.86[JPT][hapmap]
rs2274396	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs2274399	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28626340	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28680827	0.86[ASN][1000 genomes]
rs35065854	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35184650	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35201135	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35613410	0.88[ASN][1000 genomes]
rs3814860	0.86[JPT][hapmap]
rs4902528	0.91[JPT][hapmap]
rs4902569	0.90[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs4902570	0.90[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs4902622	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4902648	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6571919	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7140164	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7143646	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7148150	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7150735	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7152341	0.86[JPT][hapmap]
rs7153482	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7161403	0.82[JPT][hapmap]
rs719455	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs8004348	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8004716	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8006321	0.86[JPT][hapmap]
rs8018717	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs910370	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs956108	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs956109	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9671943	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9671953	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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 target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10162550	PPP2R3C	cis	parietal	SCAN
rs10162550	CTAGE5	cis	multi-tissue	Pritchard
rs10162550	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39737000-39741000	Weak transcription	Spleen	Spleen
2	chr14:39737000-39751800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:39737200-39741600	Weak transcription	Esophagus	oesophagus
4	chr14:39737800-39748800	Weak transcription	Right Ventricle	heart
5	chr14:39737800-39750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:39737800-39763800	Weak transcription	Gastric	stomach
7	chr14:39738000-39740600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr14:39738000-39740600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr14:39738000-39740800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr14:39738000-39740800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr14:39738000-39740800	Weak transcription	Brain Germinal Matrix	brain
12	chr14:39738000-39742400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr14:39738000-39742600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr14:39738000-39744400	Weak transcription	Right Atrium	heart
15	chr14:39738000-39748800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr14:39738000-39750600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr14:39738000-39752000	Weak transcription	Stomach Mucosa	stomach
18	chr14:39738000-39763800	Weak transcription	HSMM	muscle
19	chr14:39738200-39741000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr14:39738200-39741000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr14:39738200-39741000	Weak transcription	Fetal Stomach	stomach
22	chr14:39738200-39742000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr14:39738200-39745000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:39738200-39747000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr14:39738200-39748800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr14:39738200-39748800	Weak transcription	Fetal Kidney	kidney
27	chr14:39738200-39748800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr14:39738200-39748800	Weak transcription	Osteobl	bone
29	chr14:39738200-39751800	Weak transcription	Colonic Mucosa	Colon
30	chr14:39738200-39751800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr14:39738200-39759200	Weak transcription	NH-A	brain
32	chr14:39738200-39763800	Weak transcription	Brain Angular Gyrus	brain
33	chr14:39738200-39763800	Weak transcription	HSMMtube	muscle
34	chr14:39738200-39766200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:39738200-39813800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:39738600-39763800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr14:39738800-39740800	Weak transcription	Primary B cells from cord blood	blood
38	chr14:39738800-39747800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr14:39738800-39748800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:39738800-39748800	Weak transcription	Adipose Nuclei	Adipose
41	chr14:39738800-39748800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr14:39738800-39748800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr14:39738800-39764800	Weak transcription	NHDF-Ad	bronchial
44	chr14:39739000-39740800	Weak transcription	Fetal Intestine Large	intestine
45	chr14:39739000-39741000	Weak transcription	Thymus	Thymus
46	chr14:39739000-39741200	Weak transcription	Psoas Muscle	Psoas
47	chr14:39739000-39746400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr14:39739000-39747200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr14:39739000-39748800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr14:39739000-39751800	Weak transcription	Brain Anterior Caudate	brain

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