Variant report

Variant	rs12255810
Chromosome Location	chr10:90640290-90640291
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	TAF1	chr10:90639558-90641029	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr10:90639586-90641828	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr10:90639480-90641613	U87	brain:	n/a	n/a
4	SP4	chr10:90640010-90640592	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:90639409-90641040	GM12892	blood:	n/a	n/a
6	POLR2A	chr10:90639936-90640714	PFSK-1	brain:	n/a	n/a
7	MAX	chr10:90639494-90640977	A549	lung:	n/a	chr10:90640816-90640826
8	POLR2A	chr10:90639614-90640945	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:90639531-90641494	GM18951	blood:	n/a	n/a
10	REST	chr10:90640198-90640790	SK-N-SH	brain:	n/a	n/a
11	TAF1	chr10:90640232-90640880	GM12892	blood:	n/a	n/a
12	CTCF	chr10:90640021-90640328	NHEK	skin:	n/a	n/a
13	BHLHE40	chr10:90639378-90640927	GM12878	blood:	n/a	chr10:90640674-90640690
14	MXI1	chr10:90639555-90641039	GM12878	blood:	n/a	n/a
15	POLR2A	chr10:90640037-90641039	MCF10A-Er-Src	breast:	n/a	n/a
16	RELA	chr10:90639656-90640919	GM19193	blood:	n/a	n/a
17	POLR2A	chr10:90639993-90640759	MCF-7	breast:	n/a	n/a
18	ETS1	chr10:90640003-90640612	A549	lung:	n/a	chr10:90640490-90640506
19	POLR2A	chr10:90639757-90640952	MCF-7	breast:	n/a	n/a
20	STAT1	chr10:90639768-90640950	GM12878	blood:	n/a	chr10:90640658-90640666
21	E2F6	chr10:90639821-90640855	H1-hESC	embryonic stem cell:	n/a	chr10:90639917-90639927 chr10:90639920-90639930 chr10:90640546-90640553
22	RAD21	chr10:90639998-90640720	IMR90	lung:	n/a	chr10:90640670-90640684
23	MXI1	chr10:90639810-90640803	HepG2	liver:	n/a	n/a
24	FOXA1	chr10:90640265-90640571	T-47D	breast:	n/a	n/a
25	WRNIP1	chr10:90639531-90640975	GM12878	blood:	n/a	n/a
26	PAX5	chr10:90640264-90640591	GM12891	blood:	n/a	chr10:90640406-90640415
27	RAD21	chr10:90640126-90640336	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr10:90640263-90640734	HepG2	liver:	n/a	n/a
29	CTCF	chr10:90640140-90640290	HCT-116	colon:	n/a	n/a
30	TAF1	chr10:90639624-90640943	GM12878	blood:	n/a	n/a
31	RAD21	chr10:90639665-90640999	ECC-1	luminal epithelium:	n/a	chr10:90640670-90640684
32	POLR2A	chr10:90639563-90641024	GM12891	blood:	n/a	n/a
33	CTCF	chr10:90640140-90640290	WI-38	lung:	n/a	n/a
34	YY1	chr10:90639765-90640791	GM12891	blood:	n/a	chr10:90639922-90639931 chr10:90639917-90639931 chr10:90639919-90639928 chr10:90640598-90640607 chr10:90639919-90639930
35	TCF3	chr10:90639660-90640760	GM12878	blood:	n/a	n/a
36	TCF12	chr10:90639595-90641139	A549	lung:	n/a	n/a
37	CTCF	chr10:90640033-90640450	GM19238	blood:	n/a	n/a
38	MAX	chr10:90639806-90640952	HepG2	liver:	n/a	chr10:90640816-90640826
39	TAF1	chr10:90639721-90640483	GM12891	blood:	n/a	n/a
40	CTCF	chr10:90640180-90640330	AG04450	lung:	n/a	n/a
41	MTA3	chr10:90639449-90640307	GM12878	blood:	n/a	n/a
42	CTCF	chr10:90640031-90640480	Fibrobl	skin:	n/a	n/a
43	RFX5	chr10:90640228-90640709	HepG2	liver:	n/a	n/a
44	MYC	chr10:90640258-90640663	GM12878	blood:	n/a	n/a
45	GABPA	chr10:90640016-90640765	MCF-7	breast:	n/a	n/a
46	MAX	chr10:90639660-90640949	MCF-7	breast:	n/a	chr10:90640816-90640826
47	POLR2A	chr10:90639293-90641628	GM12892	blood:	n/a	n/a
48	E2F4	chr10:90640210-90640601	GM12878	blood:	n/a	chr10:90640546-90640553
49	HMGN3	chr10:90640049-90640545	K562	blood:	n/a	n/a
50	ZKSCAN1	chr10:90639600-90640908	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:90639968..90640523-chr12:50794439..50795346,2	Hela-S3	cervix:
2	chr10:90640051..90640725-chr11:82868123..82868682,2	NB4	blood:
3	chr10:90639734..90640291-chr9:86595257..86596036,2	Hela-S3	cervix:
4	chr1:179851373..179852293-chr10:90640061..90640817,2	Hela-S3	cervix:
5	chr1:226496799..226497354-chr10:90639813..90640457,2	Hela-S3	cervix:
6	chr10:90640024..90640648-chrX:134165843..134166387,2	NB4	blood:
7	chr10:90640148..90640826-chr5:52284747..52285544,2	Hela-S3	cervix:
8	chr10:90640063..90640881-chr5:81267682..81268245,2	Hela-S3	cervix:
9	chr10:90639301..90642051-chr10:90749823..90751899,2	MCF-7	breast:
10	chr10:90634887..90637855-chr10:90638729..90640945,2	MCF-7	breast:
11	chr10:90640047..90640717-chr9:133569002..133569668,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIPM-1	chr10:90639981-90640395	NONHSAT015480

Variant related genes	Relation type
STAMBPL1	TF binding region
ENSG00000165119	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000164171	Chromatin interaction
ENSG00000107796	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000183814	Chromatin interaction
ENSG00000152348	Chromatin interaction
ENSG00000026103	Chromatin interaction
ENSG00000134590	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000130713	Chromatin interaction
ENSG00000234256	Chromatin interaction
ENSG00000165494	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11202862	1.00[ASW][hapmap]
rs11817978	1.00[ASW][hapmap]
rs2231782	1.00[ASN][1000 genomes]
rs3218615	1.00[MEX][hapmap]
rs7895496	1.00[MEX][hapmap]
rs7912706	1.00[ASW][hapmap]
rs7921400	1.00[MEX][hapmap]
rs9663252	1.00[MEX][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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90639000-90642200	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:90639200-90640800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:90639200-90641200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:90639200-90642000	Active TSS	Brain Cingulate Gyrus	brain
5	chr10:90639200-90642000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr10:90639200-90642400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:90639400-90640400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
8	chr10:90639400-90641000	Active TSS	NH-A	brain
9	chr10:90639400-90641200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr10:90639400-90641200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr10:90639400-90641200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr10:90639400-90641200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr10:90639400-90641200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr10:90639400-90641200	Active TSS	HSMM	muscle
15	chr10:90639400-90641400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:90639400-90641400	Active TSS	Brain Angular Gyrus	brain
17	chr10:90639400-90641400	Active TSS	Brain Substantia Nigra	brain
18	chr10:90639400-90641400	Active TSS	HSMMtube	muscle
19	chr10:90639400-90641800	Active TSS	Ovary	ovary
20	chr10:90639400-90642000	Active TSS	Right Atrium	heart
21	chr10:90639400-90642400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr10:90639600-90640400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr10:90639600-90640600	Active TSS	Brain Hippocampus Middle	brain
24	chr10:90639600-90640800	Active TSS	Aorta	Aorta
25	chr10:90639600-90640800	Active TSS	Stomach Mucosa	stomach
26	chr10:90639600-90640800	Active TSS	K562	blood
27	chr10:90639600-90641000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr10:90639600-90641000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr10:90639600-90641000	Active TSS	Esophagus	oesophagus
30	chr10:90639600-90641000	Active TSS	Gastric	stomach
31	chr10:90639600-90641000	Active TSS	Pancreas	Pancrea
32	chr10:90639600-90641000	Active TSS	Small Intestine	intestine
33	chr10:90639600-90641000	Active TSS	Spleen	Spleen
34	chr10:90639600-90641200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:90639600-90641200	Active TSS	Left Ventricle	heart
36	chr10:90639600-90641400	Active TSS	Right Ventricle	heart
37	chr10:90639600-90641600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:90639600-90641600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr10:90639600-90641600	Active TSS	Colonic Mucosa	Colon
40	chr10:90639600-90641600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr10:90639600-90641800	Active TSS	Colon Smooth Muscle	Colon
42	chr10:90639600-90643000	Active TSS	A549	lung
43	chr10:90639800-90640400	Flanking Active TSS	Lung	lung
44	chr10:90639800-90640600	Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr10:90639800-90640600	Active TSS	Placenta Amnion	Placenta Amnion
46	chr10:90639800-90640800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:90639800-90640800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr10:90639800-90640800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr10:90639800-90640800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr10:90639800-90640800	Active TSS	Primary B cells from peripheral blood	blood

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