Variant report

Variant	rs2188119
Chromosome Location	chr12:46310296-46310297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46308594..46311088-chr12:46324841..46326949,2	K562	blood:
2	chr12:46292762..46294729-chr12:46309457..46311445,2	K562	blood:
3	chr12:46302175..46304891-chr12:46306625..46310381,4	MCF-7	breast:
4	chr12:46307711..46310365-chr12:46312983..46315898,2	K562	blood:
5	chr12:46309788..46315756-chr12:46316862..46321300,7	K562	blood:
6	chr12:46305718..46310311-chr12:46310347..46314383,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139218	Chromatin interaction

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

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

rs_ID	r²[population]
rs12426716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1291625	0.98[AMR][1000 genomes];0.96[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];0.83[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]
rs1366023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];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]
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];0.83[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];0.96[MKK][hapmap];0.96[TSI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];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];0.96[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];0.88[EUR][1000 genomes];0.96[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];0.96[MKK][hapmap];0.96[TSI][hapmap]
rs247927	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.83[AMR][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];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][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];0.96[MKK][hapmap];0.96[TSI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];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];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[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];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582578	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[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[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[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[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]
rs7961085	0.94[AFR][1000 genomes];0.98[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[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975444	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	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
rs2188119	NELL2	cis	cerebellum	SCAN
rs2188119	PDZRN4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46245400-46318600	Weak transcription	Small Intestine	intestine
2	chr12:46259000-46316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:46269000-46319200	Weak transcription	Spleen	Spleen
4	chr12:46269400-46316200	Weak transcription	Brain Angular Gyrus	brain
5	chr12:46269800-46315800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:46273400-46311200	Weak transcription	Right Ventricle	heart
7	chr12:46273400-46314400	Weak transcription	Brain Substantia Nigra	brain
8	chr12:46281400-46328800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:46286000-46321200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:46286200-46318000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:46286600-46316600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:46287200-46322000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:46289000-46315400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:46289200-46315400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:46289200-46316600	Weak transcription	K562	blood
16	chr12:46289400-46314600	Weak transcription	Hela-S3	cervix
17	chr12:46290200-46316200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:46290200-46320400	Weak transcription	Fetal Brain Male	brain
19	chr12:46290200-46320600	Weak transcription	Psoas Muscle	Psoas
20	chr12:46290200-46322200	Weak transcription	Esophagus	oesophagus
21	chr12:46290400-46315800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:46290400-46318000	Weak transcription	Brain Anterior Caudate	brain
23	chr12:46290400-46325800	Weak transcription	Aorta	Aorta
24	chr12:46290600-46313600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:46290600-46315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:46290600-46316600	Weak transcription	Pancreas	Pancrea
27	chr12:46290600-46316600	Weak transcription	HepG2	liver
28	chr12:46290600-46316800	Weak transcription	Lung	lung
29	chr12:46290600-46318000	Weak transcription	Ovary	ovary
30	chr12:46291000-46316400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:46291400-46320600	Weak transcription	Fetal Brain Female	brain
32	chr12:46291400-46321600	Weak transcription	Colonic Mucosa	Colon
33	chr12:46291800-46315200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:46292000-46315400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:46292200-46312000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:46292200-46312400	Weak transcription	Fetal Kidney	kidney
37	chr12:46294200-46312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:46295600-46311800	Weak transcription	Fetal Intestine Small	intestine
39	chr12:46295600-46312000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:46295600-46316600	Weak transcription	Gastric	stomach
41	chr12:46295800-46311200	Weak transcription	Left Ventricle	heart
42	chr12:46299000-46320200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
44	chr12:46299200-46310800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:46299200-46311200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:46299200-46315600	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:46299400-46312200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:46299400-46316400	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:46299600-46311000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:46299600-46311200	Weak transcription	Liver	Liver

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