Variant report

Variant	rs11168220
Chromosome Location	chr12:48135590-48135591
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	NFIC	chr12:48134931-48135776	ECC-1	luminal epithelium:	n/a	n/a
2	MYC	chr12:48135573-48135706	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:48135140-48135674	HL-60	blood:	n/a	n/a
4	CTCF	chr12:48135560-48135710	GM12872	blood:	n/a	n/a
5	SMC3	chr12:48134962-48137002	SK-N-SH	brain:	n/a	chr12:48136185-48136199
6	TCF12	chr12:48135001-48135682	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr12:48135150-48136817	SK-N-SH	brain:	n/a	chr12:48136186-48136199 chr12:48136177-48136187 chr12:48136185-48136206 chr12:48136183-48136201
8	NFIC	chr12:48134899-48135742	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr12:48134925-48135627	SK-N-SH	brain:	n/a	n/a
10	ZKSCAN1	chr12:48135226-48136519	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:48135037-48135700	HL-60	blood:	n/a	n/a
12	TCF12	chr12:48134919-48135777	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr12:48135573-48136750	HCT-116	colon:	n/a	chr12:48136186-48136199 chr12:48136177-48136187 chr12:48136185-48136206 chr12:48136183-48136201
14	NFIC	chr12:48135016-48135641	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr12:48133458-48135692	ECC-1	luminal epithelium:	n/a	n/a
16	RAD21	chr12:48134688-48138386	SK-N-SH	brain:	n/a	chr12:48137969-48137978 chr12:48136189-48136201 chr12:48136184-48136203 chr12:48137970-48137982 chr12:48136189-48136199 chr12:48136185-48136199 chr12:48137965-48137984 chr12:48136187-48136200 chr12:48137968-48137981
17	TEAD4	chr12:48135010-48135611	ECC-1	luminal epithelium:	n/a	n/a
18	EP300	chr12:48135059-48135621	ECC-1	luminal epithelium:	n/a	n/a
19	EP300	chr12:48134891-48135747	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48135430..48136483-chr12:48166395..48167426,3	K562	blood:
2	chr12:48134835..48139182-chr12:48152118..48155732,5	MCF-7	breast:
3	chr12:48135112..48136657-chr12:48212167..48214385,2	K562	blood:
4	chr12:48128880..48137705-chr12:48169546..48175532,12	K562	blood:
5	chr12:48135569..48136676-chr12:48166473..48167804,4	MCF-7	breast:
6	chr12:48135061..48136993-chr12:48147045..48149552,2	MCF-7	breast:
7	chr12:48116790..48119550-chr12:48135315..48137472,2	K562	blood:
8	chr12:48133209..48136160-chr12:48165338..48168109,2	K562	blood:
9	chr12:48099217..48102022-chr12:48134946..48137757,2	K562	blood:
10	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000111405	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000005175	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10875683	0.89[ASN][1000 genomes]
rs11168211	0.88[EUR][1000 genomes]
rs11168212	0.89[ASN][1000 genomes]
rs11168219	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11830795	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11834770	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1235152	0.82[ASN][1000 genomes]
rs12812960	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12828238	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2003471	0.82[ASN][1000 genomes]
rs2074531	0.82[ASN][1000 genomes]
rs2074532	0.82[ASN][1000 genomes]
rs2074533	0.85[AFR][1000 genomes]
rs2074534	0.84[AFR][1000 genomes]
rs2238144	0.87[ASN][1000 genomes]
rs2239188	0.82[ASN][1000 genomes]
rs2283345	0.82[ASN][1000 genomes]
rs2285830	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764015	0.82[ASN][1000 genomes]
rs3764016	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764018	0.82[ASN][1000 genomes]
rs3764019	0.82[ASN][1000 genomes]
rs3764020	0.82[ASN][1000 genomes]
rs4505143	0.87[ASN][1000 genomes]
rs6580635	0.82[ASN][1000 genomes]
rs6580636	0.82[ASN][1000 genomes]
rs7133585	0.89[ASN][1000 genomes]
rs726588	0.87[ASN][1000 genomes]
rs7306556	0.82[ASN][1000 genomes]
rs757284	0.89[ASN][1000 genomes]
rs7967336	0.82[ASN][1000 genomes]
rs7967546	0.82[ASN][1000 genomes]
rs7976708	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48127600-48135800	Enhancers	Fetal Muscle Trunk	muscle
2	chr12:48128200-48135600	Enhancers	Right Atrium	heart
3	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:48129200-48137600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:48129400-48138600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:48129800-48137600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
9	chr12:48130400-48137600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:48130600-48138800	Weak transcription	Fetal Intestine Large	intestine
11	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
12	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
13	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:48131600-48136400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr12:48131600-48136600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr12:48131800-48141000	Weak transcription	Gastric	stomach
17	chr12:48132000-48136200	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:48132200-48136400	Enhancers	Primary B cells from peripheral blood	blood
19	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:48132600-48136000	Enhancers	Primary B cells from cord blood	blood
21	chr12:48132600-48136400	Enhancers	Adipose Nuclei	Adipose
22	chr12:48132800-48136600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr12:48133200-48135800	Enhancers	Left Ventricle	heart
24	chr12:48133400-48135600	Enhancers	Lung	lung
25	chr12:48133400-48135800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr12:48133400-48135800	Enhancers	Right Ventricle	heart
27	chr12:48133400-48136000	Enhancers	Fetal Muscle Leg	muscle
28	chr12:48133600-48135600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:48133600-48135600	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr12:48133600-48135600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr12:48133600-48135600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr12:48133600-48135800	Enhancers	Duodenum Mucosa	Duodenum
33	chr12:48133600-48136000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr12:48133600-48136000	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr12:48133600-48136200	Enhancers	Stomach Smooth Muscle	stomach
36	chr12:48133600-48136400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:48133600-48136400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:48133600-48136400	Enhancers	Brain Cingulate Gyrus	brain
39	chr12:48133600-48136400	Enhancers	Fetal Heart	heart
40	chr12:48133600-48136600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:48133600-48136600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:48133600-48136600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:48133600-48137000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr12:48133800-48135800	Enhancers	Spleen	Spleen
45	chr12:48133800-48136000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr12:48134000-48135600	Enhancers	Fetal Brain Male	brain
47	chr12:48134000-48135600	Enhancers	Fetal Lung	lung
48	chr12:48134000-48135800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:48134000-48135800	Enhancers	HUVEC	blood vessel
50	chr12:48134000-48136000	Enhancers	Primary hematopoietic stem cells	blood

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