Variant report

Variant	rs7647411
Chromosome Location	chr3:112063250-112063251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10511311	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12106673	0.84[CEU][hapmap];0.81[MEX][hapmap]
rs12106967	0.84[CEU][hapmap]
rs12491166	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072567	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13084367	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13090468	0.83[CEU][hapmap]
rs13098589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317243	0.81[CEU][hapmap]
rs1343852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272022	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276772	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2399416	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34345145	0.80[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs4682103	0.83[CHB][hapmap]
rs4682399	0.80[CEU][hapmap];0.84[MEX][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7647411	ZNF80	cis	cerebellum	SCAN
rs7647411	CD200	cis	cerebellum	SCAN
rs7647411	CD200	cis	parietal	SCAN

Chromatin state (count:75 , 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	chr3:112053800-112063800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:112053800-112064200	Weak transcription	Fetal Intestine Large	intestine
7	chr3:112054000-112065800	Weak transcription	Fetal Kidney	kidney
8	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:112054200-112063800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:112054200-112064000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:112054800-112063400	Weak transcription	Ovary	ovary
12	chr3:112054800-112063800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:112054800-112066400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:112054800-112076800	Weak transcription	Lung	lung
15	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:112055000-112063400	Weak transcription	Brain Germinal Matrix	brain
17	chr3:112055200-112068800	Weak transcription	Fetal Intestine Small	intestine
18	chr3:112055400-112063800	Weak transcription	Fetal Stomach	stomach
19	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:112056000-112063800	Weak transcription	Thymus	Thymus
22	chr3:112056200-112065400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:112056400-112064000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:112056600-112064600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:112056600-112076400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:112057800-112067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:112057800-112068800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:112058600-112067400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:112058800-112063400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:112058800-112063400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:112058800-112063800	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:112058800-112064000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:112058800-112069800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:112059000-112066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:112059200-112069000	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr3:112059600-112066600	Weak transcription	Brain Substantia Nigra	brain
37	chr3:112059600-112075000	Strong transcription	Fetal Thymus	thymus
38	chr3:112059800-112065600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:112060000-112063400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:112060200-112063800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:112060200-112064200	Weak transcription	Placenta	Placenta
42	chr3:112060800-112064000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:112061200-112083000	Weak transcription	Colonic Mucosa	Colon
44	chr3:112061400-112076000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr3:112061600-112064400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr3:112061800-112067400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:112062200-112063400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:112062200-112063400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
49	chr3:112062200-112066200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:112062200-112066600	Strong transcription	Fetal Lung	lung

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