Variant report

Variant	rs17118953
Chromosome Location	chr12:57114869-57114870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57113954-57114976	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:57114779-57115729	ECC-1	luminal epithelium:	n/a	n/a
3	SPI1	chr12:57114683-57115126	HL-60	blood:	n/a	n/a
4	POLR2A	chr12:57111849-57115834	K562	blood:	n/a	n/a
5	POLR2A	chr12:57113929-57115771	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr12:57109373-57115069	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:57109486-57115298	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:57109177-57115890	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr12:57112257-57114921	A549	lung:	n/a	n/a
10	POLR2A	chr12:57112532-57115744	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:57114459-57115001	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:57114374-57115746	MCF-7	breast:	n/a	n/a
13	POLR2A	chr12:57109283-57116293	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:57114280-57115427	K562	blood:	n/a	n/a
15	POLR2A	chr12:57114072-57115772	GM12892	blood:	n/a	n/a
16	POLR2A	chr12:57112634-57115751	K562	blood:	n/a	n/a
17	POLR2A	chr12:57113751-57115655	HepG2	liver:	n/a	n/a
18	POLR2A	chr12:57114376-57115338	ECC-1	luminal epithelium:	n/a	n/a
19	NFATC1	chr12:57114420-57115142	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:57109094-57117058	SK-N-MC	brain:	n/a	n/a
21	HEY1	chr12:57114383-57114894	K562	blood:	n/a	n/a
22	POLR2A	chr12:57114465-57114957	GM12891	blood:	n/a	n/a
23	SPI1	chr12:57114729-57114939	K562	blood:	n/a	n/a
24	SPI1	chr12:57114479-57115251	HL-60	blood:	n/a	n/a
25	POLR2A	chr12:57114395-57115822	GM12892	blood:	n/a	n/a
26	POLR2A	chr12:57114423-57114874	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:57114846-57115122	K562	blood:	n/a	n/a
28	POLR2A	chr12:57114094-57116142	K562	blood:	n/a	n/a
29	POLR2A	chr12:57114509-57114993	HCT-116	colon:	n/a	n/a
30	POLR2A	chr12:57114715-57115249	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:57112872-57115428	HL-60	blood:	n/a	n/a
32	POLR2A	chr12:57114385-57115874	HL-60	blood:	n/a	n/a
33	POLR2A	chr12:57109356-57117115	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:57114601-57115899	HepG2	liver:	n/a	n/a
35	POLR2A	chr12:57112599-57115857	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:57109233-57116354	PANC-1	pancreas:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57075341..57085478-chr12:57112447..57121011,58	MCF-7	breast:
2	chr12:57113156..57115169-chr12:57146013..57147663,2	K562	blood:
3	chr12:57091041..57092738-chr12:57114705..57116928,2	MCF-7	breast:
4	chr12:57113713..57116326-chr12:57145534..57147437,2	MCF-7	breast:
5	chr12:57038025..57041646-chr12:57113711..57120620,12	MCF-7	breast:
6	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
7	chr12:57091435..57092961-chr12:57113686..57115355,2	K562	blood:
8	chr12:57076604..57085974-chr12:57112559..57120474,46	MCF-7	breast:
9	chr12:57078475..57085183-chr12:57112918..57121559,38	K562	blood:
10	chr12:57022951..57032187-chr12:57113330..57121462,17	K562	blood:
11	chr12:57113663..57115512-chr12:57124278..57127097,2	K562	blood:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000110955	Chromatin interaction
ENSG00000207031	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000110958	Chromatin interaction
ENSG00000025423	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000196531	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11171910	0.85[GIH][hapmap]
rs11833209	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833254	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833282	0.90[AFR][1000 genomes]
rs11837737	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837790	1.00[ASW][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838315	0.81[AFR][1000 genomes]
rs12312913	0.85[GIH][hapmap]
rs12314491	0.85[GIH][hapmap]
rs17118865	0.90[ASW][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs17118901	0.88[YRI][hapmap]
rs17118921	0.81[AFR][1000 genomes]
rs4262757	0.83[AFR][1000 genomes]
rs55962252	0.89[AFR][1000 genomes]
rs56258039	0.81[AFR][1000 genomes]
rs60574031	0.88[AFR][1000 genomes]
rs7307578	0.90[ASW][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs7974103	0.89[ASW][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap]
rs7974600	0.92[YRI][hapmap]
rs7977632	0.81[ASW][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap]
rs941210	0.85[GIH][hapmap]

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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv20867	chr12:57110564-57115506	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 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	chr12:57104600-57115000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:57108400-57115400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:57108600-57117200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:57109200-57116200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:57109600-57115400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
6	chr12:57109600-57116000	Genic enhancers	Fetal Muscle Leg	muscle
7	chr12:57109600-57117000	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr12:57109600-57117000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr12:57109600-57117800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:57109800-57115800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr12:57109800-57117200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:57110200-57115400	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr12:57110200-57115800	Genic enhancers	Placenta	Placenta
14	chr12:57110200-57116800	Genic enhancers	Fetal Stomach	stomach
15	chr12:57110400-57116800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:57110400-57117600	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr12:57112000-57115400	Genic enhancers	A549	lung
18	chr12:57112000-57115600	Genic enhancers	Lung	lung
19	chr12:57112000-57116000	Genic enhancers	Fetal Intestine Small	intestine
20	chr12:57112200-57115800	Enhancers	Fetal Heart	heart
21	chr12:57112200-57117000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:57112200-57117200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:57112400-57115000	Genic enhancers	Brain Hippocampus Middle	brain
24	chr12:57112400-57115000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:57112400-57115800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:57112400-57116800	Genic enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:57112600-57115000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:57112600-57115000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:57112600-57115000	Genic enhancers	HepG2	liver
30	chr12:57112600-57115200	Strong transcription	Brain Germinal Matrix	brain
31	chr12:57112600-57115200	Genic enhancers	Right Ventricle	heart
32	chr12:57112600-57115200	Strong transcription	NH-A	brain
33	chr12:57112600-57115400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:57112600-57115400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
35	chr12:57112600-57115400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr12:57112600-57115400	Genic enhancers	Brain Anterior Caudate	brain
37	chr12:57112600-57115400	Genic enhancers	Esophagus	oesophagus
38	chr12:57112600-57115400	Strong transcription	Fetal Brain Female	brain
39	chr12:57112600-57115400	Genic enhancers	Pancreas	Pancrea
40	chr12:57112600-57115400	Genic enhancers	Rectal Mucosa Donor 29	rectum
41	chr12:57112600-57115400	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr12:57112600-57115600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:57112600-57116000	Genic enhancers	Adipose Nuclei	Adipose
44	chr12:57112600-57116000	Genic enhancers	Fetal Intestine Large	intestine
45	chr12:57112600-57116200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr12:57112600-57116200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:57112600-57116200	Genic enhancers	Brain Cingulate Gyrus	brain
48	chr12:57112600-57116400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:57112600-57116400	Genic enhancers	Left Ventricle	heart
50	chr12:57112600-57116600	Genic enhancers	Liver	Liver

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