Variant report

Variant	rs10842839
Chromosome Location	chr12:9237102-9237103
allele	C/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	E2F4	chr12:9237004-9237174	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:9236048-9237557	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9236930-9237158	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9236127..9237912-chr12:9246166..9247720,2	MCF-7	breast:
2	chr12:9217388..9219245-chr12:9235426..9237537,2	MCF-7	breast:

Variant related genes	Relation type
A2M	TF binding region
ENSG00000214851	Chromatin interaction
ENSG00000245105	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10743598	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771308	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10842849	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048839	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs113973	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1805682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193006	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216143	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226380	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226381	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226382	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226386	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226387	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226388	1.00[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226389	1.00[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226390	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226391	1.00[CEU][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs226392	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226394	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226400	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226401	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226403	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs226408	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226415	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759277	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882977	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6487584	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71453666	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295733	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7964085	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7965790	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976808	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
2	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
4	chr12:9230800-9240400	Weak transcription	Placenta	Placenta
5	chr12:9230800-9243600	Weak transcription	Colonic Mucosa	Colon
6	chr12:9232200-9264600	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:9232400-9242600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:9232400-9244600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:9234000-9237400	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:9234400-9237800	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:9234600-9239400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr12:9235000-9242800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:9235000-9253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:9235200-9241200	Weak transcription	Left Ventricle	heart
15	chr12:9235200-9242400	Weak transcription	Aorta	Aorta
16	chr12:9235200-9242400	Weak transcription	Ovary	ovary
17	chr12:9235200-9242800	Weak transcription	Fetal Stomach	stomach
18	chr12:9235200-9242800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:9235200-9242800	Weak transcription	Spleen	Spleen
20	chr12:9235200-9243000	Weak transcription	Lung	lung
21	chr12:9235200-9265800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:9235800-9241600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:9236000-9237600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:9236200-9237200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:9236200-9237200	ZNF genes & repeats	Liver	Liver
26	chr12:9236200-9237200	ZNF genes & repeats	Psoas Muscle	Psoas
27	chr12:9236200-9237400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
28	chr12:9236200-9237600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:9236200-9237600	ZNF genes & repeats	Fetal Lung	lung
30	chr12:9236400-9237400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:9236400-9237400	ZNF genes & repeats	Adipose Nuclei	Adipose
32	chr12:9236400-9237600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:9236600-9237400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:9236600-9238600	Strong transcription	HepG2	liver
35	chr12:9236600-9258800	Weak transcription	Fetal Heart	heart
36	chr12:9236800-9237400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:9236800-9238800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:9236800-9242600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:9236800-9242800	Weak transcription	Right Ventricle	heart
40	chr12:9236800-9243200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:9237000-9237800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:9237000-9238000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:9237000-9240200	Weak transcription	Colon Smooth Muscle	Colon

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