Variant report

Variant	rs764192
Chromosome Location	chr12:46363027-46363028
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46353562..46359244-chr12:46361441..46367398,6	K562	blood:
2	chr12:46361472..46363562-chr12:46382349..46384332,2	K562	blood:
3	chr12:46361732..46364124-chr12:46370348..46372099,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12423797	0.82[AFR][1000 genomes]
rs12426716	0.82[AFR][1000 genomes]
rs1291625	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1291628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366023	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1427749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17712809	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs17774927	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs183646	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2059405	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap]
rs2114844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2188119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408436	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap]
rs247927	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35123	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35124	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768662	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4768671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582578	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299892	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7309711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73097319	0.81[ASN][1000 genomes]
rs7961085	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975444	0.88[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	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv3439887	chr12:46337377-46370366	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs764192	PDZRN4	cis	cerebellum	SCAN
rs764192	NELL2	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:46329800-46371000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:46341800-46365600	Weak transcription	K562	blood
4	chr12:46342000-46364000	Weak transcription	Gastric	stomach
5	chr12:46342200-46365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:46342200-46369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:46343000-46375000	Weak transcription	NHEK	skin
8	chr12:46348600-46366200	Weak transcription	Thymus	Thymus
9	chr12:46349200-46367000	Weak transcription	Fetal Intestine Small	intestine
10	chr12:46352000-46363600	Weak transcription	Aorta	Aorta
11	chr12:46355600-46367800	Weak transcription	HMEC	breast
12	chr12:46356400-46369200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:46356600-46374200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:46357000-46364000	Weak transcription	Fetal Intestine Large	intestine
15	chr12:46357000-46366000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:46357000-46371000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:46357000-46380400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:46357200-46367000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:46357200-46369000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:46357600-46364200	Weak transcription	Hela-S3	cervix
21	chr12:46357600-46365800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr12:46357600-46367000	Weak transcription	HUVEC	blood vessel
23	chr12:46357600-46380000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:46357800-46363400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:46357800-46364000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:46357800-46365200	Weak transcription	Fetal Lung	lung
27	chr12:46357800-46365400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:46357800-46381200	Weak transcription	Fetal Kidney	kidney
29	chr12:46358000-46365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:46358200-46366000	Weak transcription	Placenta	Placenta
31	chr12:46358200-46366200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:46358400-46364600	Enhancers	Fetal Heart	heart
33	chr12:46358600-46363600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr12:46358800-46363600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr12:46358800-46364200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr12:46358800-46365000	Weak transcription	Primary T cells from cord blood	blood
37	chr12:46358800-46365600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:46358800-46380600	Weak transcription	Spleen	Spleen
39	chr12:46359000-46365000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:46359000-46367200	Weak transcription	HepG2	liver
41	chr12:46359200-46363400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:46359200-46364000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:46359200-46366000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr12:46359400-46364000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:46359400-46364000	Weak transcription	Fetal Thymus	thymus
46	chr12:46359400-46364200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:46359400-46365400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr12:46359400-46367200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:46359600-46366400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:46360000-46365200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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