Variant report

Variant	rs3766688
Chromosome Location	chr1:175151950-175151951
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	chr1:175150391..175152928-chr1:175161401..175163000,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235750	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1057239	0.88[ASW][hapmap]
rs1057246	0.88[ASW][hapmap]
rs10798341	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798342	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10912903	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11583687	0.88[ASW][hapmap]
rs12084108	0.85[ASN][1000 genomes]
rs12143530	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894709	0.88[ASW][hapmap]
rs2205603	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269650	0.81[GIH][hapmap]
rs2272784	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2685	0.88[ASW][hapmap]
rs34370567	0.88[ASW][hapmap]
rs3753554	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753555	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753557	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766681	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766683	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766684	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766685	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766687	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766692	0.85[ASN][1000 genomes]
rs3766694	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6674635	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677931	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677935	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760486	0.81[GIH][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	nsv949473	chr1:175151666-175391741	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3766688	KIFAP3	cis	cerebellum	SCAN
rs3766688	GORAB	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175129200-175159600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:175130200-175152600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:175135000-175152600	Weak transcription	Aorta	Aorta
4	chr1:175135000-175158400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:175136000-175157600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:175141000-175160200	Weak transcription	HUVEC	blood vessel
7	chr1:175141400-175158400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:175143000-175160800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:175143600-175158000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:175145800-175152600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:175146000-175157800	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr1:175146200-175159400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:175146200-175159800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:175146600-175155600	Weak transcription	Ovary	ovary
15	chr1:175146800-175160400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:175147000-175153800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:175147000-175155600	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:175147000-175156200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:175147200-175155600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:175147600-175160400	Weak transcription	Colonic Mucosa	Colon
21	chr1:175148000-175153400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:175148200-175157400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:175148200-175157600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:175148200-175157800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:175148400-175159200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:175148600-175152000	Weak transcription	Gastric	stomach
27	chr1:175148600-175152200	Weak transcription	Fetal Intestine Small	intestine
28	chr1:175148600-175154800	Genic enhancers	Primary B cells from cord blood	blood
29	chr1:175148800-175158000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:175149400-175152800	Weak transcription	Esophagus	oesophagus
31	chr1:175149600-175152200	Enhancers	HMEC	breast
32	chr1:175149800-175153600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:175149800-175153600	Weak transcription	Small Intestine	intestine
34	chr1:175150200-175152000	Strong transcription	GM12878-XiMat	blood
35	chr1:175150400-175152200	Genic enhancers	NHEK	skin
36	chr1:175150400-175153000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:175150400-175154000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr1:175150400-175154200	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr1:175150800-175154000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr1:175150800-175154200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:175151000-175152000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:175151000-175152200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:175151000-175152400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:175151000-175152600	Enhancers	K562	blood
45	chr1:175151000-175153800	Enhancers	Fetal Thymus	thymus
46	chr1:175151000-175154200	Genic enhancers	Placenta	Placenta
47	chr1:175151200-175152000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:175151200-175153200	Enhancers	Adipose Nuclei	Adipose
49	chr1:175151200-175153600	Genic enhancers	Primary T cells from cord blood	blood
50	chr1:175151200-175153800	Genic enhancers	Lung	lung

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