Variant report

Variant	rs12772460
Chromosome Location	chr10:5044096-5044097
allele	A/G
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	USF1	chr10:5043676-5044738	A549	lung:	n/a	n/a
2	BCL3	chr10:5043019-5045474	A549	lung:	n/a	chr10:5043544-5043553
3	TAF1	chr10:5043464-5044582	A549	lung:	n/a	n/a
4	POLR2A	chr10:5043151-5045162	A549	lung:	n/a	n/a
5	FOSL2	chr10:5043906-5044503	A549	lung:	n/a	n/a
6	POLR2A	chr10:5043941-5044409	HepG2	liver:	n/a	n/a
7	POLR2A	chr10:5043423-5044769	A549	lung:	n/a	n/a
8	SIN3AK20	chr10:5043096-5044595	A549	lung:	n/a	n/a
9	GATA3	chr10:5043090-5045307	A549	lung:	n/a	chr10:5043398-5043415 chr10:5043407-5043416 chr10:5043543-5043553
10	MAX	chr10:5043532-5044925	A549	lung:	n/a	n/a
11	ZBTB33	chr10:5043728-5044788	A549	lung:	n/a	chr10:5044053-5044062
12	GATA3	chr10:5043732-5044754	A549	lung:	n/a	n/a
13	REST	chr10:5043709-5044679	A549	lung:	n/a	n/a
14	SP1	chr10:5039869-5045261	A549	lung:	n/a	n/a
15	POLR2A	chr10:5043176-5044679	A549	lung:	n/a	n/a
16	REST	chr10:5043035-5045421	A549	lung:	n/a	n/a
17	POLR2A	chr10:5043407-5044146	A549	lung:	n/a	n/a
18	BCL3	chr10:5043450-5044764	A549	lung:	n/a	chr10:5043544-5043553
19	ETS1	chr10:5043622-5044749	A549	lung:	n/a	n/a
20	FOSL2	chr10:5043589-5045369	A549	lung:	n/a	n/a
21	SIN3AK20	chr10:5043231-5045188	A549	lung:	n/a	n/a
22	JUND	chr10:5043066-5044758	A549	lung:	n/a	n/a
23	SP1	chr10:5039954-5045161	A549	lung:	n/a	n/a
24	ZBTB33	chr10:5043784-5044708	A549	lung:	n/a	chr10:5044053-5044062
25	POLR2A	chr10:5044003-5044134	A549	lung:	n/a	n/a
26	TCF12	chr10:5043767-5044365	A549	lung:	n/a	n/a
27	ATF3	chr10:5043740-5045168	A549	lung:	n/a	n/a
28	SIX5	chr10:5043322-5045281	A549	lung:	n/a	n/a
29	TCF12	chr10:5042180-5045370	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5030937..5032573-chr10:5043050..5044672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239148	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10904381	1.00[ASN][1000 genomes]
rs11252863	1.00[ASN][1000 genomes]
rs11252867	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12356635	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357650	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774733	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17396032	1.00[ASN][1000 genomes]
rs61854345	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription 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	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription 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	18 gene(s)	inside rSNPs	diseases
7	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv894794	chr10:4972761-5121745	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription 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	14 gene(s)	inside rSNPs	diseases
14	nsv430122	chr10:4986040-5134511	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv825221	chr10:4999349-5046239	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	nsv549884	chr10:5037926-5065248	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1036566	chr10:5037926-5261426	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5005800-5045800	Weak transcription	HSMMtube	muscle
2	chr10:5011600-5044200	Weak transcription	Fetal Brain Female	brain
3	chr10:5019400-5044600	Weak transcription	Brain Germinal Matrix	brain
4	chr10:5021800-5044400	Weak transcription	NHDF-Ad	bronchial
5	chr10:5024400-5056800	Weak transcription	Esophagus	oesophagus
6	chr10:5024800-5044400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:5024800-5051400	Weak transcription	Fetal Intestine Small	intestine
8	chr10:5025000-5045800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:5025200-5044200	Weak transcription	K562	blood
10	chr10:5027600-5045000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr10:5027800-5045800	Weak transcription	Fetal Stomach	stomach
12	chr10:5027800-5045800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:5027800-5050600	Weak transcription	Pancreas	Pancrea
14	chr10:5028000-5045800	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:5033800-5044600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:5040000-5045200	Transcr. at gene 5' and 3'	A549	lung
17	chr10:5040000-5045600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:5041000-5044600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:5041200-5044200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr10:5041600-5045800	Weak transcription	HMEC	breast
21	chr10:5041600-5047400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:5042200-5045600	Weak transcription	Osteobl	bone
23	chr10:5043200-5045200	Active TSS	Right Atrium	heart
24	chr10:5043400-5046000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:5043800-5044200	Enhancers	Psoas Muscle	Psoas
26	chr10:5044000-5044200	Enhancers	Fetal Brain Male	brain
27	chr10:5044000-5044400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:5044000-5044400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr10:5044000-5044400	Active TSS	HepG2	liver
30	chr10:5044000-5044600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:5044000-5044600	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr10:5044000-5044800	Flanking Active TSS	Liver	Liver

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