Variant report

Variant	rs7612748
Chromosome Location	chr3:112066360-112066361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10511310	1.00[CHB][hapmap]
rs10804498	1.00[ASN][1000 genomes]
rs10934163	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10934164	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10934165	1.00[ASN][1000 genomes]
rs11709101	1.00[ASN][1000 genomes]
rs11717777	1.00[ASN][1000 genomes]
rs11720514	1.00[ASN][1000 genomes]
rs11923402	1.00[ASN][1000 genomes]
rs11926389	1.00[CHB][hapmap]
rs12489470	1.00[CHB][hapmap]
rs12489616	1.00[CHB][hapmap]
rs12497979	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12636943	1.00[CHB][hapmap]
rs13063452	1.00[CHB][hapmap]
rs13064242	1.00[CHB][hapmap]
rs13084103	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1317244	0.81[CEU][hapmap]
rs1317295	1.00[ASN][1000 genomes]
rs1317658	1.00[ASN][1000 genomes]
rs13316383	1.00[ASN][1000 genomes]
rs1388858	1.00[CHB][hapmap]
rs1388859	1.00[CHB][hapmap]
rs1492479	1.00[ASN][1000 genomes]
rs17446282	1.00[CHB][hapmap]
rs17513880	1.00[ASN][1000 genomes]
rs2399419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399422	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2633546	1.00[ASN][1000 genomes]
rs2683891	1.00[ASN][1000 genomes]
rs2683892	1.00[ASN][1000 genomes]
rs28615303	1.00[ASN][1000 genomes]
rs4234409	1.00[CHB][hapmap]
rs4234411	1.00[CHB][hapmap]
rs4321508	1.00[CHB][hapmap]
rs4347976	1.00[CHB][hapmap]
rs4434123	1.00[CHB][hapmap]
rs4507229	1.00[ASN][1000 genomes]
rs4538347	1.00[CHB][hapmap]
rs4622877	1.00[ASN][1000 genomes]
rs4638935	1.00[CHB][hapmap]
rs4682393	1.00[ASN][1000 genomes]
rs4682400	1.00[ASN][1000 genomes]
rs55748364	1.00[ASN][1000 genomes]
rs55947719	1.00[ASN][1000 genomes]
rs56008438	1.00[ASN][1000 genomes]
rs56065326	1.00[ASN][1000 genomes]
rs56364691	1.00[ASN][1000 genomes]
rs56404254	1.00[ASN][1000 genomes]
rs57998879	1.00[ASN][1000 genomes]
rs60949597	1.00[ASN][1000 genomes]
rs62262366	1.00[ASN][1000 genomes]
rs62262408	1.00[ASN][1000 genomes]
rs62262411	1.00[ASN][1000 genomes]
rs62264125	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276848	1.00[ASN][1000 genomes]
rs62278760	1.00[ASN][1000 genomes]
rs62278765	1.00[ASN][1000 genomes]
rs62278768	1.00[ASN][1000 genomes]
rs62278769	1.00[ASN][1000 genomes]
rs62278770	1.00[ASN][1000 genomes]
rs62278771	1.00[ASN][1000 genomes]
rs62278843	1.00[ASN][1000 genomes]
rs6438072	1.00[ASN][1000 genomes]
rs6775536	1.00[ASN][1000 genomes]
rs6781844	1.00[CHB][hapmap]
rs6787323	1.00[CHB][hapmap]
rs6789875	1.00[CHB][hapmap]
rs6795820	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6797177	1.00[CHB][hapmap]
rs6801795	1.00[CHB][hapmap]
rs6804836	1.00[CHB][hapmap]
rs6805112	1.00[CHB][hapmap]
rs6805397	1.00[CHB][hapmap]
rs73223638	1.00[ASN][1000 genomes]
rs7431999	1.00[CHB][hapmap]
rs7609904	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7615460	1.00[CHB][hapmap]
rs7621431	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7625249	1.00[CHB][hapmap]
rs7631673	1.00[ASN][1000 genomes]
rs7636107	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7637088	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7637676	1.00[CHB][hapmap]
rs7637682	1.00[CHB][hapmap]
rs7650962	1.00[ASN][1000 genomes]
rs7651121	1.00[ASN][1000 genomes]
rs9288939	1.00[CHB][hapmap]
rs9288942	1.00[CHB][hapmap]
rs9810170	1.00[CHB][hapmap]
rs9810421	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9816969	1.00[ASN][1000 genomes]
rs9818407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823824	1.00[ASN][1000 genomes]
rs9829698	1.00[ASN][1000 genomes]
rs9838489	1.00[CEU][hapmap]
rs9842650	0.84[CEU][hapmap]
rs9851760	1.00[ASN][1000 genomes]
rs9853669	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855755	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9871088	1.00[ASN][1000 genomes]
rs9871492	1.00[CHB][hapmap]
rs9881834	0.81[CEU][hapmap]

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	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7612748	C3orf17	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112052600-112066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
3	chr3:112053200-112066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:112054800-112066400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:112054800-112076800	Weak transcription	Lung	lung
8	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:112055200-112068800	Weak transcription	Fetal Intestine Small	intestine
10	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:112056600-112076400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:112057800-112067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:112057800-112068800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:112058600-112067400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:112058800-112069800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:112059000-112066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:112059200-112069000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr3:112059600-112066600	Weak transcription	Brain Substantia Nigra	brain
20	chr3:112059600-112075000	Strong transcription	Fetal Thymus	thymus
21	chr3:112061200-112083000	Weak transcription	Colonic Mucosa	Colon
22	chr3:112061400-112076000	Strong transcription	Primary hematopoietic stem cells	blood
23	chr3:112061800-112067400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:112062200-112066600	Strong transcription	Fetal Lung	lung
25	chr3:112062200-112067800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:112062400-112069000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:112062400-112083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:112062600-112076600	Strong transcription	Primary B cells from cord blood	blood
29	chr3:112062800-112074600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:112063000-112066800	Strong transcription	Brain Anterior Caudate	brain
31	chr3:112063200-112066400	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr3:112063200-112066400	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:112063200-112066600	Strong transcription	Adipose Nuclei	Adipose
34	chr3:112063200-112067000	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr3:112063200-112067400	Strong transcription	Aorta	Aorta
36	chr3:112063400-112066800	Strong transcription	Ovary	ovary
37	chr3:112063400-112067200	Strong transcription	Fetal Brain Female	brain
38	chr3:112063400-112067400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:112063400-112074200	Strong transcription	Brain Germinal Matrix	brain
40	chr3:112063600-112066400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:112063600-112066400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:112063600-112068600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:112063800-112067200	Strong transcription	Primary T cells from cord blood	blood
44	chr3:112063800-112067200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:112063800-112067200	Strong transcription	Fetal Stomach	stomach
46	chr3:112063800-112067200	Strong transcription	Thymus	Thymus
47	chr3:112063800-112067600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:112064000-112066800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:112064000-112067200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:112064000-112067200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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