Variant report

Variant	rs12635872
Chromosome Location	chr3:112077457-112077458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10804500	0.87[EUR][1000 genomes]
rs10934166	0.87[EUR][1000 genomes]
rs10934167	0.87[EUR][1000 genomes]
rs10934169	0.87[EUR][1000 genomes]
rs10934170	0.90[EUR][1000 genomes]
rs11708769	0.90[EUR][1000 genomes]
rs11710561	0.87[EUR][1000 genomes]
rs11712036	0.87[EUR][1000 genomes]
rs11719721	0.87[EUR][1000 genomes]
rs11917566	0.86[EUR][1000 genomes]
rs11917581	0.87[EUR][1000 genomes]
rs12629421	0.87[EUR][1000 genomes]
rs12630238	0.87[EUR][1000 genomes]
rs12630278	0.87[EUR][1000 genomes]
rs12633029	0.87[EUR][1000 genomes]
rs12634619	0.87[EUR][1000 genomes]
rs12635015	0.90[EUR][1000 genomes]
rs12639474	0.86[EUR][1000 genomes]
rs16859469	0.87[EUR][1000 genomes]
rs16859507	0.90[EUR][1000 genomes]
rs1814987	0.87[EUR][1000 genomes]
rs1879511	0.86[EUR][1000 genomes]
rs1906520	0.85[EUR][1000 genomes]
rs2895395	0.86[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs2895396	0.90[EUR][1000 genomes]
rs4355253	0.87[EUR][1000 genomes]
rs4355254	0.86[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs57025230	0.87[EUR][1000 genomes]
rs57661530	0.92[EUR][1000 genomes]
rs58425909	0.87[EUR][1000 genomes]
rs59202208	0.87[EUR][1000 genomes]
rs59744939	0.86[EUR][1000 genomes]
rs60204227	0.85[EUR][1000 genomes]
rs62264124	0.87[EUR][1000 genomes]
rs62278831	0.87[EUR][1000 genomes]
rs62278832	0.87[EUR][1000 genomes]
rs62278833	0.87[EUR][1000 genomes]
rs62278834	0.87[EUR][1000 genomes]
rs62278835	0.87[EUR][1000 genomes]
rs62278836	0.87[EUR][1000 genomes]
rs62278837	0.87[EUR][1000 genomes]
rs62278838	0.87[EUR][1000 genomes]
rs62278839	0.87[EUR][1000 genomes]
rs62278841	0.87[EUR][1000 genomes]
rs62278842	0.87[EUR][1000 genomes]
rs62278844	0.87[EUR][1000 genomes]
rs62278846	0.84[EUR][1000 genomes]
rs62278847	0.81[EUR][1000 genomes]
rs62278848	0.87[EUR][1000 genomes]
rs62278849	0.87[EUR][1000 genomes]
rs62278850	0.87[EUR][1000 genomes]
rs62278853	0.87[EUR][1000 genomes]
rs62278854	0.87[EUR][1000 genomes]
rs62278855	0.87[EUR][1000 genomes]
rs62278856	0.87[EUR][1000 genomes]
rs6764384	0.87[EUR][1000 genomes]
rs6787841	0.87[EUR][1000 genomes]
rs6788309	0.87[EUR][1000 genomes]
rs6789161	0.87[EUR][1000 genomes]
rs6801708	0.87[EUR][1000 genomes]
rs6801739	0.87[EUR][1000 genomes]
rs72950242	0.87[EUR][1000 genomes]
rs72950273	0.87[EUR][1000 genomes]
rs72952411	0.92[EUR][1000 genomes]
rs72952437	0.90[EUR][1000 genomes]
rs72952454	0.85[EUR][1000 genomes]
rs72952463	0.85[EUR][1000 genomes]
rs7639471	0.86[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs7653490	0.87[EUR][1000 genomes]
rs869042	0.87[EUR][1000 genomes]
rs9834347	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs9863371	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs9867245	0.90[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12635872	CD200	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112054800-112083000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:112055600-112080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:112061200-112083000	Weak transcription	Colonic Mucosa	Colon
4	chr3:112062400-112083000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112065600-112079600	Weak transcription	Fetal Intestine Large	intestine
6	chr3:112066000-112089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:112067000-112079400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:112067200-112079800	Weak transcription	Fetal Stomach	stomach
9	chr3:112067200-112080400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:112069200-112084000	Weak transcription	Fetal Kidney	kidney
11	chr3:112069200-112095400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:112070200-112086200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:112070600-112080400	Weak transcription	Brain Angular Gyrus	brain
14	chr3:112070600-112080400	Weak transcription	Brain Anterior Caudate	brain
15	chr3:112070600-112086200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:112070600-112088800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:112070800-112079600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:112070800-112084600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:112070800-112090600	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:112071000-112077600	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:112071000-112083000	Weak transcription	Brain Substantia Nigra	brain
22	chr3:112071200-112083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:112071800-112079400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:112072000-112080600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:112072400-112080400	Weak transcription	Fetal Brain Male	brain
26	chr3:112073000-112080400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:112073400-112079600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:112074200-112079600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:112074600-112078000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:112075200-112078200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:112076200-112077800	Active TSS	Right Ventricle	heart
32	chr3:112076200-112078200	Enhancers	Primary B cells from peripheral blood	blood
33	chr3:112076400-112077600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr3:112076400-112077600	Enhancers	H9 Cell Line	embryonic stem cell
35	chr3:112076400-112078000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
36	chr3:112076400-112078000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr3:112076600-112077600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:112076800-112077600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:112076800-112077600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:112076800-112077600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:112076800-112077600	Enhancers	Pancreas	Pancrea
42	chr3:112076800-112077600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:112076800-112077600	Enhancers	Spleen	Spleen
44	chr3:112076800-112077800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr3:112076800-112077800	Enhancers	HUVEC	blood vessel
46	chr3:112076800-112078200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
47	chr3:112076800-112078400	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr3:112077000-112077600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:112077000-112077600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:112077000-112077600	Active TSS	Left Ventricle	heart

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