Variant report

Variant	rs12248434
Chromosome Location	chr10:96306509-96306510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:96120995..96123181-chr10:96304440..96307322,3	MCF-7	breast:
2	chr10:96160448..96164371-chr10:96304138..96307716,8	MCF-7	breast:
3	chr10:96304740..96307263-chr10:96312412..96314149,2	MCF-7	breast:
4	chr10:96159758..96162488-chr10:96305268..96307065,2	K562	blood:
5	chr10:96290006..96295152-chr10:96302633..96306565,5	K562	blood:
6	chr10:96305623..96306527-chr6:64282239..64282872,2	Hela-S3	cervix:
7	chr10:96305075..96307344-chr10:96312057..96315359,3	K562	blood:
8	chr10:96306294..96309021-chr10:96316197..96318090,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000119969	Chromatin interaction
ENSG00000108239	Chromatin interaction
ENSG00000112245	Chromatin interaction
ENSG00000173145	Chromatin interaction
ENSG00000266680	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1047625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509675	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs1065026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882479	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882493	1.00[ASN][1000 genomes]
rs11187919	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187921	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187999	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188055	1.00[ASN][1000 genomes]
rs11188067	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs11591641	1.00[ASN][1000 genomes]
rs11815200	1.00[ASN][1000 genomes]
rs12243416	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs12246393	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249418	1.00[CHB][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs12255683	0.81[GIH][hapmap]
rs12260063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262606	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12263131	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12268719	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12269412	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12771899	1.00[ASN][1000 genomes]
rs12785061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1334596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209671	1.00[ASN][1000 genomes]
rs2296683	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs34122982	0.84[EUR][1000 genomes]
rs35695457	1.00[ASN][1000 genomes]
rs35891778	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7077277	1.00[ASN][1000 genomes]
rs7099637	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7898763	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7904979	1.00[ASN][1000 genomes]
rs7905907	1.00[ASN][1000 genomes]
rs7911131	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7918101	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs9733708	1.00[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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12248434	NOC3L	cis	parietal	SCAN
rs12248434	DNTT	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96304200-96306800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr10:96304200-96306800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:96304200-96307000	Active TSS	A549	lung
4	chr10:96304400-96306600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:96304400-96306600	Active TSS	NHDF-Ad	bronchial
6	chr10:96304400-96306800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr10:96304400-96306800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr10:96304400-96306800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:96304400-96307000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:96304400-96307000	Active TSS	Muscle Satellite Cultured Cells	--
11	chr10:96304400-96307200	Active TSS	GM12878-XiMat	blood
12	chr10:96304400-96307400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr10:96304400-96307400	Active TSS	K562	blood
14	chr10:96304400-96307600	Active TSS	NHLF	lung
15	chr10:96304400-96309000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:96304600-96306600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:96304600-96306600	Active TSS	Fetal Intestine Large	intestine
18	chr10:96304600-96306600	Active TSS	HSMMtube	muscle
19	chr10:96304600-96306600	Active TSS	NHEK	skin
20	chr10:96304600-96306800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:96304600-96306800	Active TSS	Fetal Intestine Small	intestine
22	chr10:96304600-96307000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr10:96304600-96307000	Active TSS	Brain Germinal Matrix	brain
24	chr10:96304600-96307000	Active TSS	Fetal Kidney	kidney
25	chr10:96304600-96307000	Active TSS	Fetal Stomach	stomach
26	chr10:96304600-96307200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr10:96304600-96307200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr10:96304600-96307400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr10:96304600-96307400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:96304600-96307400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr10:96304800-96306600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:96304800-96306600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr10:96304800-96306600	Active TSS	Stomach Mucosa	stomach
34	chr10:96304800-96307000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr10:96304800-96307000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:96304800-96307000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:96304800-96307200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr10:96304800-96307600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:96304800-96307800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:96305000-96306600	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr10:96305000-96306800	Active TSS	Rectal Smooth Muscle	rectum
42	chr10:96305800-96306600	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr10:96305800-96306600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr10:96305800-96306600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr10:96305800-96306800	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr10:96305800-96306800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr10:96305800-96308000	Transcr. at gene 5' and 3'	Dnd41	blood
48	chr10:96306000-96306600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr10:96306000-96306600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr10:96306000-96306600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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