Variant report

Variant	rs7484839
Chromosome Location	chr12:122070961-122070962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122070584..122072114-chr12:122100684..122102629,2	K562	blood:
2	chr12:122070438..122071974-chr12:122238811..122240422,2	MCF-7	breast:
3	chr12:122048372..122050638-chr12:122068464..122071383,2	K562	blood:
4	chr12:122068936..122071796-chr12:122073971..122075897,3	K562	blood:

Variant related genes	Relation type
ENSG00000212694	Chromatin interaction

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

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

rs_ID	r²[population]
rs10770183	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840610	0.91[AFR][1000 genomes]
rs10840648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840650	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840651	0.83[AFR][1000 genomes]
rs11043296	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11043306	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043308	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11043316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs11614109	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12304179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12305333	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12313273	0.83[MEX][hapmap]
rs12315280	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12319633	0.91[AFR][1000 genomes]
rs12322922	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1983269	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28594507	0.84[ASW][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap]
rs28637676	1.00[CEU][hapmap]
rs3741595	0.84[ASW][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes]
rs4760125	0.85[AMR][1000 genomes]
rs6486795	0.83[MEX][hapmap]
rs7313601	0.82[MEX][hapmap]
rs7398511	0.85[AMR][1000 genomes]
rs7485243	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7487117	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7484839	NME2P1	cis	cerebellum	SCAN
rs7484839	KCNC2	trans	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122065400-122080800	Weak transcription	Aorta	Aorta
2	chr12:122065600-122071400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:122066000-122078800	Weak transcription	Fetal Brain Female	brain
4	chr12:122066200-122071400	Enhancers	Placenta	Placenta
5	chr12:122066200-122071400	Enhancers	Lung	lung
6	chr12:122066200-122071600	Enhancers	Liver	Liver
7	chr12:122066200-122090400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:122066400-122071600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:122066400-122071600	Enhancers	Psoas Muscle	Psoas
10	chr12:122066400-122096600	Weak transcription	Brain Anterior Caudate	brain
11	chr12:122066800-122071400	Genic enhancers	Fetal Intestine Small	intestine
12	chr12:122067600-122071600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:122067800-122071200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:122067800-122071200	Genic enhancers	Fetal Thymus	thymus
15	chr12:122067800-122071400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:122067800-122071400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr12:122067800-122096600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:122068000-122071400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:122068000-122072600	Weak transcription	HSMM	muscle
20	chr12:122068200-122071200	Enhancers	HUVEC	blood vessel
21	chr12:122068200-122071400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:122068200-122078800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:122068400-122071400	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr12:122068600-122071600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr12:122069000-122071600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr12:122069200-122071600	Enhancers	Fetal Intestine Large	intestine
27	chr12:122069400-122071400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr12:122069400-122071600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr12:122069400-122074200	Weak transcription	Dnd41	blood
30	chr12:122069400-122082200	Weak transcription	NHDF-Ad	bronchial
31	chr12:122069400-122090800	Weak transcription	Hela-S3	cervix
32	chr12:122069600-122071600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:122069800-122071000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
34	chr12:122069800-122071000	Genic enhancers	K562	blood
35	chr12:122069800-122071400	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr12:122069800-122071400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:122069800-122071400	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr12:122069800-122071600	Enhancers	Fetal Stomach	stomach
39	chr12:122070000-122071000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:122070000-122071000	Enhancers	Brain Hippocampus Middle	brain
41	chr12:122070000-122071200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:122070000-122071200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr12:122070000-122071200	Enhancers	Ovary	ovary
44	chr12:122070000-122071200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr12:122070000-122071200	Enhancers	NHLF	lung
46	chr12:122070000-122071400	Enhancers	H1 Cell Line	embryonic stem cell
47	chr12:122070000-122071400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr12:122070000-122071400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:122070000-122071400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:122070000-122071400	Enhancers	Colon Smooth Muscle	Colon

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