Variant report

Variant	rs12468286
Chromosome Location	chr2:10862188-10862189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10857464..10859699-chr2:10860592..10863283,2	MCF-7	breast:
2	chr2:10828658..10831241-chr2:10859513..10862984,4	MCF-7	breast:
3	chr2:10856794..10860140-chr2:10861984..10865438,3	K562	blood:
4	chr2:10861917..10863725-chr2:10871850..10873491,2	MCF-7	breast:
5	chr2:10856794..10858384-chr2:10861984..10864074,2	K562	blood:

Variant related genes	Relation type
ENSG00000236162	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000243819	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10929692	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12619522	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12998055	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs13034991	0.87[ASN][1000 genomes]
rs35978327	0.85[ASN][1000 genomes]
rs881572	0.86[LWK][hapmap]

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	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12468286	NOL10	cis	parietal	SCAN
rs12468286	ATP6V1C2	cis	brain	BrainEAC

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10860400-10862600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
2	chr2:10860800-10862600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr2:10860800-10862600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
4	chr2:10861000-10862200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:10861000-10862200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
6	chr2:10861000-10862400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr2:10861000-10862400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:10861000-10862400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:10861000-10862600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr2:10861000-10862600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:10861000-10862600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
12	chr2:10861000-10862600	Bivalent/Poised TSS	Fetal Brain Female	brain
13	chr2:10861000-10862800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:10861000-10862800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:10861200-10862200	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:10861200-10862200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:10861200-10862400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr2:10861200-10862400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
19	chr2:10861200-10862400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:10861200-10862400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:10861200-10862400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
22	chr2:10861200-10862600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:10861200-10862600	Bivalent/Poised TSS	A549	lung
24	chr2:10861200-10863000	Enhancers	Spleen	Spleen
25	chr2:10861400-10862200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:10861400-10862200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:10861400-10862200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr2:10861400-10862200	Flanking Active TSS	Psoas Muscle	Psoas
29	chr2:10861400-10862200	Bivalent/Poised TSS	Thymus	Thymus
30	chr2:10861400-10862200	Flanking Bivalent TSS/Enh	HMEC	breast
31	chr2:10861400-10862400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr2:10861400-10862400	Active TSS	Aorta	Aorta
33	chr2:10861400-10862400	Flanking Active TSS	Liver	Liver
34	chr2:10861400-10862400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:10861400-10862400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
36	chr2:10861400-10862400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
37	chr2:10861600-10862200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr2:10861600-10862200	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:10861600-10862200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:10861600-10862200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:10861600-10862400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:10861600-10862400	Active TSS	Gastric	stomach
43	chr2:10861800-10862200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:10861800-10862200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
45	chr2:10861800-10862200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:10861800-10862200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:10861800-10862200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr2:10861800-10862200	Transcr. at gene 5' and 3'	Right Atrium	heart
49	chr2:10861800-10862200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr2:10861800-10862400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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