Variant report

Variant	rs12027008
Chromosome Location	chr1:150349768-150349769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150348697..150350794-chr1:150354817..150356893,2	K562	blood:
2	chr1:150344693..150350764-chr1:150356084..150361525,10	MCF-7	breast:
3	chr1:150343989..150346170-chr1:150348649..150351860,4	K562	blood:
4	chr1:150343057..150346056-chr1:150346785..150349871,3	MCF-7	breast:
5	chr1:150347618..150350415-chr1:150352527..150354380,2	K562	blood:
6	chr1:150348425..150350004-chr1:150352890..150354588,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10494266	0.81[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap]
rs10888585	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11205363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205372	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12032387	0.90[EUR][1000 genomes]
rs12119249	0.82[ASN][1000 genomes]
rs12119250	1.00[ASW][hapmap]
rs12137280	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16837432	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2275780	1.00[ASW][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes]
rs59325647	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59844700	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61819393	1.00[AFR][1000 genomes]
rs6685125	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs956796	1.00[ASW][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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12027008	CELF3	cis	cerebellum	SCAN
rs12027008	TMOD4	cis	cerebellum	SCAN
rs12027008	CTSS	cis	cerebellum	SCAN
rs12027008	MRPS21	cis	cerebellum	SCAN
rs12027008	MRPS21	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150338400-150405200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:150339400-150372800	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:150339400-150390600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:150339600-150356400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:150339600-150359800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:150339600-150372800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:150339800-150368600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:150339800-150390000	Weak transcription	Thymus	Thymus
9	chr1:150340000-150362000	Weak transcription	Primary B cells from cord blood	blood
10	chr1:150340000-150416800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:150340600-150366800	Weak transcription	Fetal Brain Female	brain
12	chr1:150342800-150361600	Weak transcription	Fetal Thymus	thymus
13	chr1:150343400-150378000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:150343600-150349800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:150343600-150361400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:150343800-150359400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:150343800-150378600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:150344000-150361600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:150345200-150350600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:150345400-150351200	Weak transcription	Fetal Intestine Small	intestine
21	chr1:150345400-150358600	Weak transcription	Fetal Intestine Large	intestine
22	chr1:150346800-150358200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:150346800-150359600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:150346800-150361600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:150347000-150355800	Weak transcription	Fetal Brain Male	brain
26	chr1:150347000-150358800	Weak transcription	Small Intestine	intestine
27	chr1:150347000-150392400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:150347200-150353800	Weak transcription	Right Atrium	heart
29	chr1:150347200-150353800	Weak transcription	Right Ventricle	heart
30	chr1:150347200-150354800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:150347200-150356200	Weak transcription	Liver	Liver
32	chr1:150347200-150357200	Weak transcription	Ovary	ovary
33	chr1:150347200-150358000	Weak transcription	Aorta	Aorta
34	chr1:150347200-150359600	Weak transcription	Dnd41	blood
35	chr1:150347200-150360000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:150347200-150360000	Weak transcription	Pancreas	Pancrea
37	chr1:150347200-150361000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:150347200-150361400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:150347200-150361600	Weak transcription	Psoas Muscle	Psoas
40	chr1:150347200-150362000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:150347200-150372400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:150347200-150380000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:150347400-150359200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:150347800-150358800	Weak transcription	Primary T cells from cord blood	blood
45	chr1:150347800-150361600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:150347800-150362200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:150348000-150356200	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:150348000-150390400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:150348400-150372600	Weak transcription	Hela-S3	cervix
50	chr1:150348600-150356200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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