Variant report

Variant	rs12106967
Chromosome Location	chr3:112060758-112060759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10511311	0.84[CEU][hapmap]
rs12106673	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13069751	0.89[EUR][1000 genomes]
rs13069935	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13070091	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13090468	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs13092081	0.87[EUR][1000 genomes]
rs13095299	0.86[EUR][1000 genomes]
rs13098589	0.84[CEU][hapmap]
rs13100916	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1317243	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879513	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1879514	0.83[ASN][1000 genomes]
rs2272022	0.84[CEU][hapmap]
rs2399412	0.87[EUR][1000 genomes]
rs2399416	0.84[CEU][hapmap]
rs4682398	0.86[EUR][1000 genomes]
rs4682399	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs6438064	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6438065	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6762106	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6773206	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6780745	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6787547	0.81[ASN][1000 genomes]
rs6798354	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6798486	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6805117	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6805142	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6808365	0.83[ASN][1000 genomes]
rs7639471	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs7639794	0.82[CHB][hapmap]
rs7647411	0.84[CEU][hapmap]
rs8179893	0.87[EUR][1000 genomes]
rs8179913	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9755930	0.83[ASN][1000 genomes]
rs9814721	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9823309	0.83[ASN][1000 genomes]
rs9834347	0.87[CHB][hapmap]
rs9852176	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9856838	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9863371	0.82[JPT][hapmap]
rs9990215	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9990216	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs9990220	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12106967	CD200	cis	cerebellum	SCAN
rs12106967	CD200	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112052600-112062400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112052600-112066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
4	chr3:112053200-112062200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112053200-112066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:112053800-112063800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:112053800-112064200	Weak transcription	Fetal Intestine Large	intestine
9	chr3:112054000-112065800	Weak transcription	Fetal Kidney	kidney
10	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:112054200-112063800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:112054200-112064000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:112054800-112060800	Enhancers	Brain Angular Gyrus	brain
14	chr3:112054800-112061800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:112054800-112063400	Weak transcription	Ovary	ovary
16	chr3:112054800-112063800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:112054800-112066400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:112054800-112076800	Weak transcription	Lung	lung
19	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:112055000-112063400	Weak transcription	Brain Germinal Matrix	brain
21	chr3:112055200-112068800	Weak transcription	Fetal Intestine Small	intestine
22	chr3:112055400-112062200	Weak transcription	Fetal Lung	lung
23	chr3:112055400-112063800	Weak transcription	Fetal Stomach	stomach
24	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:112055800-112076400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:112056000-112063800	Weak transcription	Thymus	Thymus
27	chr3:112056200-112065400	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:112056400-112064000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:112056600-112064600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:112056600-112076400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:112057600-112063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:112057800-112063200	Weak transcription	Fetal Brain Male	brain
33	chr3:112057800-112067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:112057800-112068800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:112058400-112060800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:112058600-112062200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:112058600-112067400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:112058800-112062200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:112058800-112062200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:112058800-112062200	Weak transcription	Left Ventricle	heart
41	chr3:112058800-112063000	Weak transcription	Brain Anterior Caudate	brain
42	chr3:112058800-112063200	Weak transcription	Adipose Nuclei	Adipose
43	chr3:112058800-112063200	Weak transcription	Aorta	Aorta
44	chr3:112058800-112063200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:112058800-112063400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:112058800-112063400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:112058800-112063800	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:112058800-112064000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:112058800-112069800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:112059000-112066600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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