Variant report

Variant	rs11717954
Chromosome Location	chr3:136112109-136112110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136111355..136112233-chr3:136471072..136471651,2	MCF-7	breast:
2	chr3:136108896..136113105-chr3:136468716..136472551,4	K562	blood:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1070232	0.87[JPT][hapmap]
rs10804640	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10935181	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935182	1.00[ASW][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10935183	0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10935184	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1145106	0.94[JPT][hapmap]
rs1153877	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11715257	0.94[JPT][hapmap]
rs11719310	0.83[EUR][1000 genomes]
rs11915629	0.91[AMR][1000 genomes]
rs12492510	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12630999	0.87[JPT][hapmap]
rs12635723	0.93[JPT][hapmap]
rs1279086	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs1279425	0.87[JPT][hapmap]
rs1279831	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1279840	0.87[JPT][hapmap]
rs1394092	0.87[JPT][hapmap]
rs1711161	0.87[JPT][hapmap]
rs1711171	0.87[JPT][hapmap]
rs2655008	0.94[JPT][hapmap]
rs3755636	0.87[JPT][hapmap]
rs4678269	0.81[EUR][1000 genomes]
rs4678428	0.87[JPT][hapmap]
rs4678433	0.87[JPT][hapmap]
rs480162	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs483465	0.87[JPT][hapmap]
rs517319	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs518972	1.00[ASW][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs521746	1.00[ASW][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs527888	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs548288	0.87[JPT][hapmap]
rs553018	0.81[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs556788	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes]
rs56235965	0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs571513	0.87[JPT][hapmap]
rs576771	0.81[JPT][hapmap]
rs589092	0.89[ASW][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap]
rs595532	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs606725	0.87[JPT][hapmap]
rs619605	0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs650326	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes]
rs654237	1.00[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs655748	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs655836	1.00[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66691851	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs667920	0.87[JPT][hapmap]
rs6791611	0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes]
rs6794351	0.87[JPT][hapmap]
rs681783	0.81[AMR][1000 genomes]
rs695983	0.94[JPT][hapmap]
rs696081	0.81[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs696516	0.94[JPT][hapmap]
rs696518	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs696520	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs698269	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs698270	0.94[JPT][hapmap]
rs699165	0.87[JPT][hapmap]
rs711972	0.97[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs711975	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs73222302	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73226190	0.82[EUR][1000 genomes]
rs7432375	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap]
rs7620314	0.92[CHB][hapmap];0.86[CHD][hapmap]
rs7621025	0.87[JPT][hapmap]
rs833752	0.87[JPT][hapmap]
rs834304	0.96[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs834305	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs838202	0.81[AMR][1000 genomes]
rs864437	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs866758	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs900048	0.94[JPT][hapmap]
rs940174	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9714347	0.82[EUR][1000 genomes]
rs9854084	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11717954	DBR1	cis	cerebellum	SCAN
rs11717954	PCCB	cis	parietal	SCAN
rs11717954	PCCB	cis	multi-tissue	Pritchard
rs11717954	PCCB	Cis_1M	lymphoblastoid	RTeQTL
rs11717954	SPSB4	cis	cerebellum	SCAN
rs11717954	PCCB	cis	cerebellum	SCAN
rs11717954	PCCB	cis	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136054600-136172000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:136063400-136139000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:136063400-136139000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:136063600-136139200	Weak transcription	Pancreas	Pancrea
5	chr3:136069400-136121200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:136069600-136138800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:136069600-136139400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:136069800-136118800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:136069800-136159600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:136070800-136112200	Weak transcription	Aorta	Aorta
11	chr3:136070800-136121400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:136075000-136137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:136075800-136160200	Weak transcription	Brain Germinal Matrix	brain
14	chr3:136079400-136174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:136081200-136118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:136084400-136123200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:136085600-136116400	Weak transcription	Fetal Intestine Large	intestine
18	chr3:136085800-136116400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:136085800-136139200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:136085800-136174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:136086000-136112200	Weak transcription	Liver	Liver
22	chr3:136086000-136128400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:136086000-136136000	Weak transcription	HSMM	muscle
24	chr3:136086200-136174800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:136086400-136116800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:136088400-136121200	Weak transcription	Thymus	Thymus
27	chr3:136093200-136117000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:136094600-136115800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:136095600-136116200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:136095600-136117200	Weak transcription	Placenta	Placenta
31	chr3:136095600-136121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:136095600-136132400	Weak transcription	Left Ventricle	heart
33	chr3:136095600-136132600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:136095600-136134400	Weak transcription	Adipose Nuclei	Adipose
35	chr3:136095600-136137800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:136095800-136116600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:136095800-136118800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:136095800-136121200	Weak transcription	Fetal Thymus	thymus
39	chr3:136095800-136122800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:136095800-136131600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:136095800-136135200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:136095800-136139200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:136096000-136115800	Weak transcription	Dnd41	blood
44	chr3:136096000-136132800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:136096000-136138200	Weak transcription	Lung	lung
46	chr3:136096800-136132600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:136096800-136133800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:136097000-136115400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:136097200-136116200	Weak transcription	Primary B cells from cord blood	blood
50	chr3:136097800-136132000	Weak transcription	Primary T cells from cord blood	blood

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