Variant report

Variant	rs12692440
Chromosome Location	chr2:11508494-11508495
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr2:11508107-11508686	ECC-1	luminal epithelium:	n/a	chr2:11508385-11508402 chr2:11508385-11508401
2	NFIC	chr2:11507959-11508697	SK-N-SH	brain:	n/a	chr2:11508385-11508402 chr2:11508385-11508401
3	PBX3	chr2:11508080-11508603	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11483340..11487694-chr2:11505828..11510815,5	K562	blood:
2	chr2:11484922..11486828-chr2:11507256..11509884,2	K562	blood:
3	chr2:11508308..11513224-chr2:11514143..11518077,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230952	TF binding region
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10170598	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10170791	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10182588	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10195908	0.94[ASN][1000 genomes]
rs10202323	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10929734	0.81[JPT][hapmap]
rs12692438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12692439	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12692441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12993210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13024110	0.94[CHB][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs35029584	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4280434	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4533449	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4641909	0.95[ASN][1000 genomes]
rs4668722	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4668723	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6432189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6708718	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6708945	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6711409	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6711414	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6716724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6719739	0.94[ASN][1000 genomes]
rs6721881	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6756145	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7420679	0.94[ASN][1000 genomes]
rs7581184	0.85[JPT][hapmap]
rs7595700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12692440	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11505400-11514400	Enhancers	Fetal Intestine Large	intestine
2	chr2:11505600-11511600	Enhancers	Fetal Intestine Small	intestine
3	chr2:11505800-11511000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:11506000-11509000	Weak transcription	Lung	lung
5	chr2:11506000-11509400	Weak transcription	Spleen	Spleen
6	chr2:11506000-11511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:11506000-11514600	Weak transcription	K562	blood
8	chr2:11506800-11511000	Enhancers	HepG2	liver
9	chr2:11507200-11509000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr2:11507200-11511200	Enhancers	Duodenum Mucosa	Duodenum
11	chr2:11507400-11508800	Enhancers	Fetal Lung	lung
12	chr2:11507400-11516200	Enhancers	Stomach Mucosa	stomach
13	chr2:11507600-11508800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:11507600-11508800	Enhancers	Brain Germinal Matrix	brain
15	chr2:11507600-11509000	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr2:11507800-11508600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:11507800-11508600	Enhancers	A549	lung
18	chr2:11507800-11508800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:11507800-11509600	Enhancers	Fetal Stomach	stomach
20	chr2:11508000-11508600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr2:11508000-11508800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:11508000-11508800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:11508000-11508800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:11508000-11508800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr2:11508000-11508800	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr2:11508000-11508800	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr2:11508000-11508800	Active TSS	Right Atrium	heart
28	chr2:11508000-11508800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr2:11508000-11508800	Flanking Active TSS	HUVEC	blood vessel
30	chr2:11508000-11509800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:11508200-11508600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:11508200-11508600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:11508200-11508600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr2:11508200-11508600	Flanking Active TSS	Liver	Liver
35	chr2:11508200-11508600	Active TSS	Brain Angular Gyrus	brain
36	chr2:11508200-11508600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:11508200-11508600	Flanking Active TSS	Ovary	ovary
38	chr2:11508200-11508600	Flanking Active TSS	Psoas Muscle	Psoas
39	chr2:11508200-11508600	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr2:11508200-11508600	Flanking Active TSS	NH-A	brain
41	chr2:11508200-11508600	Flanking Active TSS	NHDF-Ad	bronchial
42	chr2:11508200-11508600	Flanking Active TSS	NHLF	lung
43	chr2:11508200-11508800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:11508200-11508800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:11508200-11508800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:11508200-11508800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:11508200-11508800	Active TSS	Aorta	Aorta
48	chr2:11508200-11508800	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr2:11508200-11508800	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr2:11508200-11508800	Flanking Active TSS	Fetal Brain Female	brain

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