Variant report

Variant	rs3769866
Chromosome Location	chr2:179361205-179361206
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179341915..179343963-chr2:179361012..179363425,2	K562	blood:

Variant related genes	Relation type
ENSG00000079150	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1001238	0.86[CHB][hapmap]
rs10207436	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10930831	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12052983	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[ASN][1000 genomes]
rs13411588	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1559908	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1560221	0.86[CHB][hapmap]
rs16866334	1.00[JPT][hapmap]
rs16866342	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866400	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs16866420	0.86[CHB][hapmap]
rs1863671	0.80[ASN][1000 genomes]
rs1978580	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2016615	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042996	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2059691	0.85[JPT][hapmap]
rs2114582	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2163009	0.86[CHB][hapmap]
rs2249737	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2288322	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2303536	1.00[JPT][hapmap];0.87[TSI][hapmap]
rs2303537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2366751	0.86[CHB][hapmap]
rs2886712	0.87[ASN][1000 genomes]
rs33998881	0.83[ASN][1000 genomes]
rs3731750	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3731754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752689	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs3769864	0.81[CHB][hapmap]
rs3813250	0.81[CHB][hapmap]
rs3829746	0.86[CHB][hapmap]
rs4894017	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4894018	0.94[CEU][hapmap]
rs4894020	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4894029	0.86[CHB][hapmap]
rs60488846	0.83[ASN][1000 genomes]
rs6704545	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6710856	0.91[ASN][1000 genomes]
rs6723399	0.84[ASN][1000 genomes]
rs6726043	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6735077	0.81[ASN][1000 genomes]
rs6739142	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs6753709	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs6758838	0.90[ASN][1000 genomes]
rs7575643	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7577862	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7587593	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7588593	0.83[ASN][1000 genomes]
rs7589679	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7598228	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7600176	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs7602597	1.00[ASW][hapmap];0.93[CEU][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8179648	0.95[JPT][hapmap];0.81[TSI][hapmap]
rs9288019	0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs957875	0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs967507	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9808377	0.86[CHB][hapmap]
rs9967820	1.00[JPT][hapmap];0.83[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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1002693	chr2:179357045-179365143	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3769866	FKBP7	cis	lymphoblastoid	seeQTL
rs3769866	ATP2C2	trans	parietal	SCAN
rs3769866	PLEKHA3	cis	Lymphoblastoid	GTEx
rs3769866	PLEKHA3	cis	lymphoblastoid	seeQTL
rs3769866	PRKRA	cis	lymphoblastoid	seeQTL
rs3769866	PRKRA	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:179347400-179363000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:179347400-179369400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:179347600-179371000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:179349800-179364200	Weak transcription	Hela-S3	cervix
6	chr2:179350400-179364200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:179350400-179371600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:179350400-179371600	Strong transcription	Dnd41	blood
9	chr2:179350400-179372400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:179350400-179372400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:179350400-179384400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:179350600-179371200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr2:179350600-179372200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:179350800-179370600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr2:179350800-179371600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:179350800-179372000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr2:179350800-179372000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:179351000-179368800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:179352800-179372200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:179353000-179361800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:179353400-179369000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:179353600-179371600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:179353800-179368400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:179354000-179362600	Strong transcription	HepG2	liver
25	chr2:179354000-179371600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:179354400-179361600	Strong transcription	Osteobl	bone
27	chr2:179354400-179371400	Strong transcription	Placenta	Placenta
28	chr2:179354400-179371600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr2:179354400-179372000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:179354600-179370000	Strong transcription	Liver	Liver
31	chr2:179354600-179373000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:179354600-179373000	Strong transcription	HSMM	muscle
33	chr2:179354800-179361800	Strong transcription	Brain Anterior Caudate	brain
34	chr2:179354800-179362800	Strong transcription	NHDF-Ad	bronchial
35	chr2:179355000-179368000	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:179355200-179361800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:179355200-179362400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:179355200-179362600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:179355200-179362600	Strong transcription	HSMMtube	muscle
40	chr2:179355200-179369000	Strong transcription	Fetal Intestine Large	intestine
41	chr2:179356000-179364600	Strong transcription	Thymus	Thymus
42	chr2:179356000-179367200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:179356000-179368400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:179356000-179368400	Strong transcription	Primary B cells from cord blood	blood
45	chr2:179356800-179361600	Strong transcription	K562	blood
46	chr2:179357200-179361800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:179357400-179361400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:179357600-179368600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:179358200-179361400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr2:179358200-179361400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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