Variant report

Variant	rs3816779
Chromosome Location	chr3:47543389-47543390
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	chr3:47517236..47519106-chr3:47543060..47545522,2	K562	blood:
2	chr3:47537303..47543925-chr3:47549598..47557776,11	K562	blood:

Variant related genes	Relation type
ENSG00000163832	Chromatin interaction
ENSG00000114650	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1038394	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865946	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs11130128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130129	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130132	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130133	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11130137	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11705957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs11707895	0.93[EUR][1000 genomes]
rs11710121	0.88[CEU][hapmap]
rs11711265	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11711824	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11712445	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11713413	0.90[EUR][1000 genomes]
rs11716763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11719877	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11914795	0.84[EUR][1000 genomes]
rs11914913	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914932	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11925823	0.80[EUR][1000 genomes]
rs12486969	0.80[EUR][1000 genomes]
rs12489046	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490058	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492433	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12495169	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs12497225	0.81[EUR][1000 genomes]
rs12630641	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12632132	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12636851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13059519	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13064843	0.81[EUR][1000 genomes]
rs13075233	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1531875	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1564760	0.81[GIH][hapmap];0.90[YRI][hapmap]
rs17080872	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs17410853	0.88[CEU][hapmap]
rs17411375	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs17784882	1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs1872164	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2062278	0.81[EUR][1000 genomes]
rs2101247	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2159400	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs2291298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs295428	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap]
rs295433	0.95[YRI][hapmap]
rs295449	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs295458	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[LWK][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs295461	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs34634681	0.92[EUR][1000 genomes]
rs3736177	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4599332	0.93[EUR][1000 genomes]
rs4858811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4858824	1.00[CEU][hapmap]
rs4858856	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4858868	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4858893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4858894	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56032309	0.81[EUR][1000 genomes]
rs57346147	0.81[EUR][1000 genomes]
rs59586735	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60369822	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62248599	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62248603	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62248605	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62260710	0.95[EUR][1000 genomes]
rs62260711	0.95[EUR][1000 genomes]
rs62260741	0.90[EUR][1000 genomes]
rs6765990	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780013	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs6787422	0.81[EUR][1000 genomes]
rs6790763	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6792461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792488	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73081205	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628631	0.98[EUR][1000 genomes]
rs7649234	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651194	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7651762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs807932	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap]
rs878659	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs922957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs9683033	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9683177	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3816779	NCKIPSD	cis	cerebellum	SCAN
rs3816779	AMIGO3	cis	cerebellum	SCAN
rs3816779	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs3816779	IFRD2	cis	parietal	SCAN
rs3816779	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs3816779	HYAL2	cis	cerebellum	SCAN
rs3816779	SCAP	cis	parietal	SCAN
rs3816779	CCDC12	cis	cerebellum	SCAN
rs3816779	PRKAR2A	cis	cerebellum	SCAN
rs3816779	C3orf75	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47517800-47544400	Weak transcription	Small Intestine	intestine
2	chr3:47532000-47546400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:47534200-47547000	Strong transcription	Dnd41	blood
4	chr3:47534400-47546000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:47534400-47546200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:47534600-47546000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:47534600-47553000	Strong transcription	Fetal Thymus	thymus
8	chr3:47534800-47549400	Weak transcription	Fetal Heart	heart
9	chr3:47534800-47552400	Strong transcription	Fetal Intestine Small	intestine
10	chr3:47534800-47553200	Strong transcription	Fetal Stomach	stomach
11	chr3:47535200-47546200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:47535200-47546200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:47535200-47546200	Strong transcription	Thymus	Thymus
14	chr3:47535200-47547000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:47535200-47553000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:47535400-47546400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr3:47535400-47546400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:47535400-47546400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:47535600-47546600	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:47535600-47547000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:47535600-47552800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:47535800-47546600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:47536200-47544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:47536200-47546400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr3:47536200-47553200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:47536400-47546000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:47536400-47546000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:47536400-47546200	Strong transcription	Liver	Liver
29	chr3:47536400-47546400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:47536400-47546400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:47536400-47546800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:47536400-47547000	Strong transcription	HepG2	liver
33	chr3:47536600-47543400	Strong transcription	Ovary	ovary
34	chr3:47536600-47544000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:47536600-47544400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:47536600-47546000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:47536600-47546000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:47536600-47546000	Strong transcription	Colonic Mucosa	Colon
39	chr3:47536600-47546000	Strong transcription	Fetal Intestine Large	intestine
40	chr3:47536600-47546000	Strong transcription	Left Ventricle	heart
41	chr3:47536600-47546000	Strong transcription	Pancreas	Pancrea
42	chr3:47536600-47546000	Strong transcription	GM12878-XiMat	blood
43	chr3:47536600-47546000	Strong transcription	NHLF	lung
44	chr3:47536600-47546000	Strong transcription	Osteobl	bone
45	chr3:47536600-47546200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:47536600-47546200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:47536600-47546200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:47536600-47546200	Strong transcription	Adipose Nuclei	Adipose
49	chr3:47536600-47546200	Strong transcription	Aorta	Aorta
50	chr3:47536600-47546200	Strong transcription	Brain Anterior Caudate	brain

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