Variant report

Variant	rs848596
Chromosome Location	chr2:36803863-36803864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11886145	0.80[ASN][1000 genomes]
rs11899523	0.84[ASN][1000 genomes]
rs2276671	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs3770793	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs3770796	0.82[ASN][1000 genomes]
rs3821150	0.83[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7570763	0.83[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs848597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848598	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848600	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs848601	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848610	0.92[ASN][1000 genomes]
rs848614	0.86[ASN][1000 genomes]
rs848619	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs848622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848623	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848624	0.96[ASN][1000 genomes]
rs848627	0.88[ASN][1000 genomes]
rs848630	0.96[ASN][1000 genomes]
rs848635	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs848636	0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs848638	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs848639	0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs848640	0.93[ASN][1000 genomes]
rs861919	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs848596	CRIM1	cis	cerebellum	SCAN
rs848596	FEZ2	cis	multi-tissue	Pritchard
rs848596	FEZ2	cis	cerebellum	SCAN
rs848596	FEZ2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:36773000-36811200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:36776600-36804800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:36776600-36804800	Weak transcription	Fetal Brain Female	brain
5	chr2:36779400-36805000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:36780000-36804800	Weak transcription	Brain Germinal Matrix	brain
7	chr2:36782000-36805400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:36783200-36805000	Weak transcription	K562	blood
9	chr2:36783400-36805000	Weak transcription	GM12878-XiMat	blood
10	chr2:36788600-36805200	Weak transcription	Left Ventricle	heart
11	chr2:36789000-36804800	Weak transcription	Fetal Kidney	kidney
12	chr2:36789200-36807000	Weak transcription	Aorta	Aorta
13	chr2:36790200-36818000	Strong transcription	Fetal Intestine Large	intestine
14	chr2:36790400-36806600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:36790800-36812000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:36791000-36807600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:36791200-36804400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:36791200-36805400	Weak transcription	Small Intestine	intestine
19	chr2:36791800-36810400	Weak transcription	Right Atrium	heart
20	chr2:36792000-36806600	Weak transcription	Spleen	Spleen
21	chr2:36792200-36810400	Weak transcription	Colonic Mucosa	Colon
22	chr2:36792200-36824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:36792800-36811400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:36793000-36806000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:36793200-36804600	Weak transcription	Right Ventricle	heart
26	chr2:36793200-36806600	Weak transcription	Esophagus	oesophagus
27	chr2:36793200-36811200	Weak transcription	Pancreas	Pancrea
28	chr2:36793200-36816600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:36793400-36804800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:36795800-36809600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:36796000-36805000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:36796000-36818000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:36796200-36805400	Weak transcription	Thymus	Thymus
34	chr2:36796200-36807400	Weak transcription	Ovary	ovary
35	chr2:36796800-36818200	Weak transcription	Brain Substantia Nigra	brain
36	chr2:36797000-36804800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr2:36797000-36804800	Weak transcription	HSMMtube	muscle
38	chr2:36797000-36805000	Weak transcription	Hela-S3	cervix
39	chr2:36797000-36807400	Weak transcription	Fetal Heart	heart
40	chr2:36797000-36808200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:36797000-36814200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr2:36797600-36808800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:36797800-36805200	Weak transcription	Brain Angular Gyrus	brain
44	chr2:36797800-36813400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:36798000-36809600	Strong transcription	HSMM	muscle
46	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr2:36798400-36806400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:36798600-36806600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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