Variant report

Variant	rs900048
Chromosome Location	chr3:136218930-136218931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136216747..136218980-chr3:136221671..136224312,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1070230	0.84[AFR][1000 genomes]
rs1070232	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs10935182	1.00[JPT][hapmap]
rs10935183	0.94[JPT][hapmap]
rs10935184	0.93[JPT][hapmap]
rs10935186	0.86[JPT][hapmap]
rs1145101	0.89[MEX][hapmap]
rs1145106	0.80[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs11715257	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs11717954	0.94[JPT][hapmap]
rs11919030	0.87[JPT][hapmap]
rs12489577	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12492510	0.94[JPT][hapmap]
rs12630999	0.86[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs12635723	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs12637102	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1279086	0.93[JPT][hapmap]
rs13068119	0.80[CEU][hapmap];0.94[MEX][hapmap]
rs1394092	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1711161	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1711170	0.81[JPT][hapmap]
rs1711171	0.85[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap]
rs2062322	0.87[JPT][hapmap]
rs2655008	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs34602896	0.83[MEX][hapmap]
rs34967300	0.80[CEU][hapmap];0.94[MEX][hapmap]
rs3856637	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs4408829	0.87[JPT][hapmap]
rs4521165	0.93[JPT][hapmap]
rs4678433	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4678437	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs4678438	0.87[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs483465	0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs518972	0.93[JPT][hapmap]
rs521746	0.94[JPT][hapmap]
rs553018	0.87[JPT][hapmap]
rs556788	0.93[JPT][hapmap]
rs571513	1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs595532	0.87[JPT][hapmap]
rs619605	1.00[JPT][hapmap]
rs6439646	0.84[AFR][1000 genomes]
rs6439649	0.93[JPT][hapmap]
rs650326	0.93[JPT][hapmap]
rs654237	0.87[JPT][hapmap]
rs655836	1.00[JPT][hapmap]
rs667920	1.00[CHB][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap]
rs6791142	0.87[JPT][hapmap]
rs6791611	0.94[JPT][hapmap]
rs6794351	0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6808312	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs695983	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs696081	0.93[JPT][hapmap]
rs696516	0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs696517	0.94[MEX][hapmap]
rs696518	1.00[JPT][hapmap]
rs696520	0.93[JPT][hapmap]
rs698270	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs699165	0.80[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs711975	0.87[JPT][hapmap]
rs711976	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7432375	0.87[JPT][hapmap]
rs7618518	0.93[JPT][hapmap]
rs7618871	0.87[JPT][hapmap]
rs7621025	0.86[ASW][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs833752	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs834304	0.92[JPT][hapmap]
rs864437	0.93[JPT][hapmap]
rs866758	0.94[JPT][hapmap]
rs9289511	1.00[CHB][hapmap]
rs940174	0.87[JPT][hapmap]
rs9757777	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9759024	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9820485	1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[ASN][1000 genomes]
rs9821478	0.89[CHB][hapmap]
rs9832056	1.00[CHB][hapmap]
rs9832813	1.00[CHB][hapmap]
rs9833207	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs9836231	0.87[JPT][hapmap]
rs9845762	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs9851986	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9854084	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes]
rs9856769	0.89[CHB][hapmap]
rs9869720	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs9883916	0.80[CEU][hapmap];0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877522	chr3:136088038-136241028	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs900048	PCCB	cis	lymphoblastoid	seeQTL
rs900048	MSL2	cis	cerebellum	SCAN
rs900048	NCK1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176600-136222800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:136176600-136224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:136176600-136224400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:136176600-136231800	Weak transcription	Psoas Muscle	Psoas
6	chr3:136176600-136240000	Weak transcription	HMEC	breast
7	chr3:136176600-136260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:136176800-136228000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
10	chr3:136177200-136236400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:136178600-136220200	Weak transcription	Fetal Brain Male	brain
12	chr3:136191000-136220000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:136192200-136225600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:136192400-136252400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:136193800-136231400	Weak transcription	NHLF	lung
17	chr3:136193800-136239200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:136195000-136220400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:136195000-136223000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:136195200-136231000	Weak transcription	Osteobl	bone
21	chr3:136195400-136231400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:136195400-136232000	Weak transcription	Right Ventricle	heart
23	chr3:136195400-136241800	Weak transcription	NH-A	brain
24	chr3:136195400-136250400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:136195600-136220200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:136195600-136224000	Weak transcription	Brain Angular Gyrus	brain
28	chr3:136203000-136224600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:136205200-136220800	Weak transcription	Fetal Brain Female	brain
30	chr3:136206400-136220400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:136208400-136230400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:136210200-136225800	Weak transcription	NHDF-Ad	bronchial
33	chr3:136210400-136220400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:136210800-136229600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:136211600-136221000	Weak transcription	HSMM	muscle
36	chr3:136211600-136232000	Weak transcription	Fetal Kidney	kidney
37	chr3:136212200-136229200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:136212400-136223200	Weak transcription	Fetal Heart	heart
40	chr3:136212400-136231000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:136212400-136232000	Weak transcription	Aorta	Aorta
42	chr3:136212400-136241600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:136212400-136249600	Weak transcription	Lung	lung
44	chr3:136212600-136220200	Weak transcription	Fetal Intestine Large	intestine
45	chr3:136212600-136248200	Weak transcription	Esophagus	oesophagus
46	chr3:136213000-136220200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:136213000-136221600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr3:136213000-136221800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:136213000-136231000	Weak transcription	Ovary	ovary
50	chr3:136213000-136239000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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