Variant report

Variant	rs36604
Chromosome Location	chr22:30340138-30340139
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr22:30340064-30340941	SK-N-SH	brain:	n/a	chr22:30340670-30340679

Variant related genes	Relation type
ENSG00000221736	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1071888	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1076137	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12168552	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12171061	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12537	0.80[CEU][hapmap]
rs131278	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap]
rs131291	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap]
rs131296	0.87[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs140135	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs140151	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17643918	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1807509	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs193473	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs193481	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2017677	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2051764	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2105870	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2349225	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs2412960	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412963	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28257	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34862234	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35705048	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36578	0.88[JPT][hapmap]
rs36580	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36586	0.82[AMR][1000 genomes]
rs36590	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36591	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36594	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36596	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36598	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36600	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36601	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36605	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36606	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36607	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788423	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3887275	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3958025	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs39712	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41162	0.82[ASW][hapmap];0.95[CEU][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs41164	0.91[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs41166	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41172	0.82[ASW][hapmap];0.83[CEU][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap]
rs41174	0.86[CEU][hapmap]
rs41175	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41179	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4239932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4820820	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4820822	0.84[EUR][1000 genomes]
rs4823055	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4823063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4993442	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752968	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5752986	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752988	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5752993	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763630	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763634	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763644	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763674	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5763675	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763680	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5763689	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763691	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs715523	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs718772	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs7286070	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7292615	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs737904	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737909	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737912	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7510705	0.82[AMR][1000 genomes]
rs8136147	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8139994	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8141404	0.95[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8141680	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9620926	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9620943	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9625873	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625874	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625878	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625879	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9625919	0.95[CEU][hapmap];0.82[AMR][1000 genomes]

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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1064489	chr22:30316627-30361881	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869764	chr22:30323649-30367813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058511	chr22:30330447-30361881	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2763694	chr22:30330459-30361881	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv588883	chr22:30333405-30365842	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs36604	KIAA1671	cis	cerebellum	SCAN
rs36604	CRYBB3	cis	parietal	SCAN
rs36604	TTC28	cis	cerebellum	SCAN
rs36604	MTMR3	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30311600-30343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:30311800-30340400	Weak transcription	HSMM	muscle
3	chr22:30313000-30343800	Weak transcription	Fetal Stomach	stomach
4	chr22:30313600-30354200	Weak transcription	Small Intestine	intestine
5	chr22:30327600-30342200	Weak transcription	Brain Angular Gyrus	brain
6	chr22:30328400-30343600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr22:30328400-30351800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr22:30330600-30342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr22:30332000-30342200	Weak transcription	Gastric	stomach
10	chr22:30332600-30345000	Weak transcription	Pancreas	Pancrea
11	chr22:30332600-30347400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr22:30332800-30340200	Weak transcription	Stomach Mucosa	stomach
13	chr22:30332800-30341000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr22:30332800-30343800	Weak transcription	Adipose Nuclei	Adipose
15	chr22:30333600-30343600	Weak transcription	Brain Anterior Caudate	brain
16	chr22:30334200-30341000	Weak transcription	Right Atrium	heart
17	chr22:30334200-30374800	Weak transcription	Thymus	Thymus
18	chr22:30334400-30341200	Weak transcription	Brain Hippocampus Middle	brain
19	chr22:30334600-30340400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr22:30334600-30341000	Weak transcription	Psoas Muscle	Psoas
21	chr22:30334600-30341000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr22:30335800-30341000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr22:30337000-30342000	Weak transcription	Brain Substantia Nigra	brain
24	chr22:30337600-30340200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr22:30338000-30340400	Weak transcription	HSMMtube	muscle
26	chr22:30338200-30340200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr22:30338200-30340200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr22:30338800-30341000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr22:30339000-30343000	Weak transcription	Brain Germinal Matrix	brain
30	chr22:30339400-30341800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr22:30339800-30340200	Enhancers	Left Ventricle	heart
32	chr22:30339800-30340200	Enhancers	Lung	lung
33	chr22:30339800-30340200	Enhancers	Spleen	Spleen
34	chr22:30339800-30340400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr22:30339800-30340400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr22:30339800-30340400	Enhancers	Primary T cells fromperipheralblood	blood
37	chr22:30339800-30340400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr22:30339800-30340400	Enhancers	Ovary	ovary
39	chr22:30339800-30340600	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr22:30339800-30340600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr22:30339800-30340800	Enhancers	Dnd41	blood
42	chr22:30339800-30341400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr22:30339800-30341800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:30339800-30342600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr22:30339800-30343200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr22:30340000-30340200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr22:30340000-30340200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr22:30340000-30340200	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr22:30340000-30340200	Enhancers	Fetal Thymus	thymus
50	chr22:30340000-30340200	Enhancers	Right Ventricle	heart

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