Variant report

Variant	rs3769605
Chromosome Location	chr2:32322456-32322457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11124272	0.85[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs11678119	0.86[MEX][hapmap]
rs11691939	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12478134	0.93[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs12614686	0.86[MEX][hapmap]
rs12991444	0.86[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs12996943	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13006495	0.93[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13013695	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs17011801	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs177082	0.93[CEU][hapmap]
rs17767988	0.81[YRI][hapmap]
rs212682	0.80[EUR][1000 genomes]
rs212684	0.84[EUR][1000 genomes]
rs212689	0.93[CEU][hapmap]
rs212736	0.87[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs212751	0.93[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212754	0.92[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs212761	0.86[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2280968	0.85[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2294178	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2366547	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs34197800	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34835885	0.92[EUR][1000 genomes]
rs375050	0.93[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3754835	0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs3769611	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs385076	0.82[CHD][hapmap]
rs410469	0.92[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs462878	0.93[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs56322034	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6543648	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6723154	0.86[MEX][hapmap]
rs6725184	0.83[CHB][hapmap]
rs6756085	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7556942	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7562653	0.92[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs7574000	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs805831	0.80[EUR][1000 genomes]
rs9789593	0.83[AMR][1000 genomes];0.88[EUR][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	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3769605	SLC30A6	cis	parietal	SCAN
rs3769605	CD5L	trans	cerebellum	SCAN
rs3769605	NLRC4	cis	lymphoblastoid	seeQTL
rs3769605	SLC30A6	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32289600-32330800	Weak transcription	Spleen	Spleen
2	chr2:32289800-32330800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:32290200-32330800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:32290400-32331000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:32290400-32353400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:32290600-32330800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:32290800-32330200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:32291000-32330400	Weak transcription	Brain Anterior Caudate	brain
9	chr2:32291000-32330800	Weak transcription	Brain Angular Gyrus	brain
10	chr2:32291000-32332600	Weak transcription	A549	lung
11	chr2:32291400-32327600	Weak transcription	Hela-S3	cervix
12	chr2:32291400-32331000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:32291600-32330800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:32291600-32330800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:32291600-32332200	Weak transcription	HUVEC	blood vessel
16	chr2:32292000-32330800	Weak transcription	Lung	lung
17	chr2:32292000-32343200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:32292400-32330800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:32292600-32353800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:32294600-32325000	Weak transcription	Dnd41	blood
21	chr2:32295000-32330200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:32295800-32353800	Weak transcription	Fetal Brain Male	brain
23	chr2:32296400-32362600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:32297600-32360600	Weak transcription	Osteobl	bone
25	chr2:32298800-32341400	Weak transcription	Small Intestine	intestine
26	chr2:32300000-32339600	Weak transcription	HepG2	liver
27	chr2:32303800-32330800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:32309800-32381200	Weak transcription	NHDF-Ad	bronchial
29	chr2:32311600-32330800	Weak transcription	Psoas Muscle	Psoas
30	chr2:32311800-32331000	Weak transcription	Gastric	stomach
31	chr2:32312000-32330800	Weak transcription	Brain Substantia Nigra	brain
32	chr2:32312200-32330800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:32312400-32330800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:32312600-32331000	Weak transcription	Colonic Mucosa	Colon
35	chr2:32313200-32360600	Weak transcription	NH-A	brain
36	chr2:32314000-32330200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:32315400-32329600	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:32315400-32330200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:32315400-32330200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:32315400-32330400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:32315400-32330400	Weak transcription	Left Ventricle	heart
42	chr2:32315400-32330600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:32315400-32330600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:32315400-32330800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:32315400-32330800	Weak transcription	Esophagus	oesophagus
46	chr2:32315400-32330800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:32315400-32330800	Weak transcription	Placenta	Placenta
48	chr2:32315400-32330800	Weak transcription	Right Ventricle	heart
49	chr2:32315400-32330800	Weak transcription	GM12878-XiMat	blood
50	chr2:32315400-32331000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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