Variant report

Variant	rs1291628
Chromosome Location	chr12:46326576-46326577
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46308594..46311088-chr12:46324841..46326949,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12426716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1291625	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1427749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17662709	1.00[YRI][hapmap]
rs17712809	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs17774927	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap]
rs183646	1.00[ASW][hapmap];0.94[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];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];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs2114844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[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[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[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[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs247927	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];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[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768660	1.00[ASW][hapmap];0.94[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]
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];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582578	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299892	0.88[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[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73097319	0.81[ASN][1000 genomes]
rs764192	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]
rs7961085	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975444	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1291628	NELL2	cis	cerebellum	SCAN
rs1291628	PDZRN4	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46281400-46328800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
3	chr12:46309400-46327400	Strong transcription	HSMM	muscle
4	chr12:46310400-46327200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:46310600-46327600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:46311000-46329000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:46311000-46329000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:46311200-46328200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:46311200-46328600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:46311400-46327000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:46311400-46329000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:46311400-46329000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:46312000-46327800	Strong transcription	Osteobl	bone
14	chr12:46312000-46328800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:46312000-46329800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:46312000-46330000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:46312000-46330000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:46312200-46348600	Strong transcription	Dnd41	blood
19	chr12:46312400-46327400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr12:46312400-46327800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:46312400-46328200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr12:46312400-46329200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:46312600-46327000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:46312600-46327800	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:46312800-46328800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:46313600-46326800	Strong transcription	Adipose Nuclei	Adipose
27	chr12:46313600-46326800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr12:46314400-46328000	Strong transcription	Fetal Thymus	thymus
29	chr12:46314600-46326800	Strong transcription	Hela-S3	cervix
30	chr12:46314600-46327000	Strong transcription	Liver	Liver
31	chr12:46314600-46327600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:46314600-46345600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:46314800-46328400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:46315000-46327600	Weak transcription	Stomach Mucosa	stomach
35	chr12:46315000-46327800	Strong transcription	Fetal Intestine Large	intestine
36	chr12:46315000-46327800	Strong transcription	GM12878-XiMat	blood
37	chr12:46315000-46328800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:46315200-46326600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:46315200-46327000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:46315200-46327600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:46315200-46327800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:46315400-46327000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:46315400-46328000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:46315600-46326600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:46315600-46327000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:46315800-46327600	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr12:46315800-46328200	Strong transcription	Placenta	Placenta
48	chr12:46316600-46343400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:46317000-46341400	Weak transcription	Gastric	stomach
50	chr12:46317400-46327600	Strong transcription	NHDF-Ad	bronchial

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