Variant report

Variant	rs1145106
Chromosome Location	chr3:136111917-136111918
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	chr3:136111355..136112233-chr3:136471072..136471651,2	MCF-7	breast:
2	chr3:136108896..136113105-chr3:136468716..136472551,4	K562	blood:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1070232	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs10935182	1.00[JPT][hapmap]
rs10935183	0.94[JPT][hapmap]
rs10935184	0.93[JPT][hapmap]
rs1145101	0.94[MEX][hapmap]
rs1153877	0.93[JPT][hapmap]
rs1154988	0.81[JPT][hapmap]
rs11715257	0.86[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs11717954	0.94[JPT][hapmap]
rs12330635	0.86[CHB][hapmap]
rs12489577	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12492510	0.94[JPT][hapmap]
rs12630999	0.84[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs12635723	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs1279086	0.93[JPT][hapmap]
rs1279425	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1279831	0.80[JPT][hapmap]
rs1279840	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs1291921	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13068119	0.88[MEX][hapmap]
rs1394092	0.80[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1618069	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1711161	0.90[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1711170	0.81[JPT][hapmap]
rs1711171	0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.85[ASN][1000 genomes]
rs17252498	0.88[MEX][hapmap]
rs1964675	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2655008	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28478252	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34967300	0.88[MEX][hapmap]
rs3755636	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs3821445	0.94[MEX][hapmap]
rs3957816	0.81[JPT][hapmap]
rs4678428	0.90[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs4678433	0.80[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs483465	0.92[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs518972	0.93[JPT][hapmap]
rs521746	0.94[JPT][hapmap]
rs548288	0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs553018	0.87[JPT][hapmap]
rs556788	0.93[JPT][hapmap]
rs571513	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs576771	0.90[CEU][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs589092	0.93[JPT][hapmap]
rs595532	0.87[JPT][hapmap]
rs606725	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap]
rs619605	1.00[JPT][hapmap]
rs645040	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs650326	0.93[JPT][hapmap]
rs654237	0.87[JPT][hapmap]
rs655720	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655836	1.00[JPT][hapmap]
rs661739	0.81[JPT][hapmap]
rs667920	0.85[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.87[ASN][1000 genomes]
rs6770476	0.81[ASN][1000 genomes]
rs6789488	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6791611	0.94[JPT][hapmap]
rs6794351	0.90[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs684773	0.81[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs687339	0.81[JPT][hapmap];0.88[MEX][hapmap]
rs695983	0.85[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.95[ASN][1000 genomes]
rs696081	0.93[JPT][hapmap]
rs696516	0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs696517	0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs696518	1.00[JPT][hapmap]
rs696520	0.93[JPT][hapmap]
rs698270	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs699165	0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap]
rs711975	0.87[JPT][hapmap]
rs7432375	0.87[JPT][hapmap]
rs7621025	1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs7644541	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8045	0.83[MEX][hapmap]
rs833752	0.80[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap]
rs834304	0.92[JPT][hapmap]
rs864437	0.93[JPT][hapmap]
rs866758	0.94[JPT][hapmap]
rs895894	0.81[JPT][hapmap]
rs900048	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]
rs9289511	1.00[CHB][hapmap]
rs940174	0.87[JPT][hapmap]
rs9757777	0.84[AMR][1000 genomes]
rs9759024	0.84[AMR][1000 genomes]
rs9809427	0.87[ASN][1000 genomes]
rs9820485	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9821478	0.86[CHB][hapmap]
rs9832056	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9832556	0.83[ASN][1000 genomes]
rs9832813	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs9845457	0.81[JPT][hapmap]
rs9848883	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs9851986	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs9854084	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes]
rs9856769	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs9869720	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs9883916	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1145106	NCK1	cis	cerebellum	SCAN
rs1145106	PCCB	cis	lymphoblastoid	seeQTL
rs1145106	NCK1	cis	parietal	SCAN
rs1145106	MSL2	cis	cerebellum	SCAN
rs1145106	PCCB	cis	cerebellum	SCAN

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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