Variant report

Variant	rs6537421
Chromosome Location	chr4:147371462-147371463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10001383	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10011222	0.81[EUR][1000 genomes]
rs10012310	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10017463	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10018860	0.86[CEU][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10024266	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs10026558	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs10030464	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10032453	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11100926	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11726588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11726594	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11734649	0.86[CEU][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11940327	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13105153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13134417	0.87[EUR][1000 genomes]
rs13134849	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13149918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13151354	0.87[EUR][1000 genomes]
rs13435029	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17769016	0.86[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2244306	0.86[MEX][hapmap]
rs2356822	0.86[MEX][hapmap]
rs2630279	0.87[GIH][hapmap];0.86[MEX][hapmap]
rs2679138	0.82[GIH][hapmap]
rs3849037	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3914629	0.86[EUR][1000 genomes]
rs4407528	0.86[MEX][hapmap]
rs4835037	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835040	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs4835307	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835312	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4835313	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4835314	0.86[CEU][hapmap];0.86[MEX][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4835315	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs4835316	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs6537419	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537423	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537424	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6537425	0.87[EUR][1000 genomes]
rs6537426	0.83[EUR][1000 genomes]
rs6812728	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815417	0.87[EUR][1000 genomes]
rs6816737	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs6819042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6829209	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs6837453	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6846498	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6849958	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs7435019	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7437083	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs7439061	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs7439429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7670877	0.87[GIH][hapmap];0.86[MEX][hapmap]
rs7687182	0.87[EUR][1000 genomes]
rs7687917	0.87[EUR][1000 genomes]
rs9992118	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9995307	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9995820	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking 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	11 gene(s)	inside rSNPs	diseases
3	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv917053	chr4:147265436-147499653	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1023868	chr4:147265443-147531626	Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv537293	chr4:147265443-147531626	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv428453	chr4:147335953-147457115	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6537421	TTC29	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147360600-147371600	Weak transcription	Primary T cells from cord blood	blood
2	chr4:147364000-147374400	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:147364400-147374200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:147364600-147374800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:147364600-147388000	Weak transcription	NHEK	skin
6	chr4:147364800-147402200	Weak transcription	Thymus	Thymus
7	chr4:147365000-147371600	Weak transcription	NHLF	lung
8	chr4:147365000-147372400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:147365000-147374000	Weak transcription	Right Ventricle	heart
10	chr4:147365200-147371600	Weak transcription	Spleen	Spleen
11	chr4:147365600-147371600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:147366600-147371600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:147366600-147379200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:147366800-147371800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:147366800-147372400	Weak transcription	Fetal Lung	lung
16	chr4:147367200-147371600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr4:147367200-147371800	Weak transcription	Pancreas	Pancrea
18	chr4:147367200-147372400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:147367200-147385000	Weak transcription	Left Ventricle	heart
20	chr4:147367400-147371600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:147367400-147372400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:147370400-147371600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:147370800-147371800	Weak transcription	Aorta	Aorta
24	chr4:147370800-147372400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:147370800-147388800	Weak transcription	Psoas Muscle	Psoas
26	chr4:147371000-147371600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:147371400-147371600	Enhancers	Primary B cells from cord blood	blood
28	chr4:147371400-147372000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr4:147371400-147372000	Flanking Active TSS	GM12878-XiMat	blood
30	chr4:147371400-147373200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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