Variant report

Variant	rs7633590
Chromosome Location	chr3:43047642-43047643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10212191	0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10510736	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13080201	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs13087788	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs17390473	0.80[CHB][hapmap]
rs17455509	0.81[CHB][hapmap];1.00[CHD][hapmap]
rs17455760	0.81[CHB][hapmap]
rs17469719	0.87[CHB][hapmap]
rs2001682	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2062517	0.92[CHB][hapmap]
rs28435122	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28548208	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2948619	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35110063	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3953390	0.91[EUR][1000 genomes]
rs531888	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs532792	0.92[CEU][hapmap];0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55701670	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55848724	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62247060	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62247061	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62247062	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442134	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644534	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6764648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783218	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[EUR][1000 genomes]
rs6792817	0.81[EUR][1000 genomes]
rs6793871	0.87[CEU][hapmap];0.80[CHB][hapmap];0.86[EUR][1000 genomes]
rs6794402	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6806427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs704918	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7616750	0.81[CHB][hapmap]
rs7619227	0.81[CHB][hapmap]
rs7624799	0.81[CHB][hapmap];1.00[CHD][hapmap]
rs7634125	0.81[CHB][hapmap]
rs7637698	0.81[CHB][hapmap]
rs7643433	0.81[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs834177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs872126	1.00[CHB][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9311332	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9812262	0.87[CHB][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs9821320	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848904	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9858123	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9863179	0.90[EUR][1000 genomes]
rs9872107	0.84[EUR][1000 genomes]
rs9874514	0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv460523	chr3:43025986-43063406	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv590150	chr3:43025986-43063406	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv432417	chr3:43045796-43098296	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7633590	HIGD1A	cis	cerebellum	SCAN
rs7633590	CCR9	cis	parietal	SCAN
rs7633590	KIF15	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43043600-43054400	Weak transcription	Placenta	Placenta
2	chr3:43043800-43054600	Weak transcription	Fetal Kidney	kidney
3	chr3:43044200-43049800	Weak transcription	Ovary	ovary
4	chr3:43044600-43052200	Weak transcription	Fetal Stomach	stomach
5	chr3:43044800-43051800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:43046600-43049000	Weak transcription	Fetal Thymus	thymus
7	chr3:43046600-43053000	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:43046800-43048000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:43046800-43048200	Enhancers	Primary T cells from cord blood	blood
10	chr3:43047000-43047800	Enhancers	Thymus	Thymus
11	chr3:43047000-43048600	Enhancers	Brain Anterior Caudate	brain
12	chr3:43047000-43049600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:43047200-43049400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr3:43047400-43047800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:43047400-43048000	Enhancers	Brain Substantia Nigra	brain
16	chr3:43047400-43048400	Enhancers	Liver	Liver
17	chr3:43047600-43047800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:43047600-43048000	Enhancers	Stomach Smooth Muscle	stomach

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