Variant report

Variant	rs4796109
Chromosome Location	chr17:34138908-34138909
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:34135622-34141134	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr17:34138880-34139201	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:34138783-34139267	GM12891	blood:	n/a	n/a
4	POLR2A	chr17:34138752-34139631	GM12892	blood:	n/a	n/a
5	POLR2A	chr17:34138414-34139641	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:34138844-34139460	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr17:34138855-34139212	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:34138821-34139493	K562	blood:	n/a	n/a
9	POLR2A	chr17:34138696-34139549	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr17:34138722-34139493	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:34138885-34139121	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr17:34135340-34139464	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr17:34138814-34139519	GM12891	blood:	n/a	n/a
14	POLR2A	chr17:34138836-34139120	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF2	chr17:34138898-34139332	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr17:34138724-34139560	GM12892	blood:	n/a	n/a
17	POLR2A	chr17:34138755-34139543	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr17:34138774-34139142	K562	blood:	n/a	n/a
19	POLR2A	chr17:34135774-34139332	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr17:34138817-34139396	GM12892	blood:	n/a	n/a
21	POLR2A	chr17:34138771-34139479	GM12892	blood:	n/a	n/a
22	POLR2A	chr17:34138708-34139347	K562	blood:	n/a	n/a
23	POLR2A	chr17:34138844-34139417	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr17:34138691-34139342	GM12878	blood:	n/a	n/a
25	ZNF274	chr17:34138524-34139173	K562	blood:	n/a	n/a
26	POLR2A	chr17:34138897-34139306	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:34123180..34125521-chr17:34136848..34139147,2	K562	blood:
2	chr17:27619493..27621031-chr17:34136580..34139229,2	MCF-7	breast:
3	chr17:34137709..34141485-chr17:34149369..34151902,3	MCF-7	breast:
4	chr17:34122737..34124680-chr17:34137626..34139147,2	K562	blood:
5	chr17:34089535..34095936-chr17:34135210..34140609,14	MCF-7	breast:
6	chr17:34138831..34141279-chr17:34143427..34145542,2	MCF-7	breast:
7	chr17:34138348..34140751-chr17:34159365..34161956,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267578	TF binding region
ENSG00000129270	Chromatin interaction
ENSG00000172660	Chromatin interaction
ENSG00000267347	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11652192	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11652536	0.81[EUR][1000 genomes]
rs11653204	0.81[EUR][1000 genomes]
rs11656556	0.81[EUR][1000 genomes]
rs11658222	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11868785	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11868801	0.81[EUR][1000 genomes]
rs2014839	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2107540	0.81[EUR][1000 genomes]
rs2306630	0.82[EUR][1000 genomes]
rs28550999	0.81[EUR][1000 genomes]
rs28739295	0.81[EUR][1000 genomes]
rs3760326	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3785764	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3809769	0.81[EUR][1000 genomes]
rs3817656	0.89[EUR][1000 genomes]
rs4251702	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4251719	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4251727	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4251729	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4251737	0.90[EUR][1000 genomes]
rs4251751	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4251752	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4251769	0.85[EUR][1000 genomes]
rs4251788	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4795088	0.80[ASN][1000 genomes]
rs4795089	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4795091	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4795092	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4795093	0.82[EUR][1000 genomes]
rs4795095	0.89[EUR][1000 genomes]
rs4796108	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4796112	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4796113	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4796114	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4796115	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4796118	0.92[EUR][1000 genomes]
rs4796119	0.89[EUR][1000 genomes]
rs4796120	0.86[EUR][1000 genomes]
rs4796124	0.81[EUR][1000 genomes]
rs4796125	0.81[EUR][1000 genomes]
rs4796126	0.80[EUR][1000 genomes]
rs4796127	0.81[EUR][1000 genomes]
rs4796129	0.84[EUR][1000 genomes]
rs4796130	0.81[EUR][1000 genomes]
rs4796131	0.81[EUR][1000 genomes]
rs56294660	0.81[EUR][1000 genomes]
rs56344830	0.82[EUR][1000 genomes]
rs59247105	0.89[EUR][1000 genomes]
rs9303691	0.89[EUR][1000 genomes]
rs9789051	0.81[EUR][1000 genomes]
rs9894083	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9898132	0.88[EUR][1000 genomes]
rs9898152	0.89[EUR][1000 genomes]
rs9900473	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9907121	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9907588	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9908907	0.89[EUR][1000 genomes]
rs9911598	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912552	0.86[EUR][1000 genomes]
rs9914401	0.89[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4796109	TAF15	Cis_1M	lymphoblastoid	RTeQTL
rs4796109	RDM1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34137000-34139400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr17:34137200-34139200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr17:34137200-34139400	Transcr. at gene 5' and 3'	K562	blood
4	chr17:34137600-34139000	Weak transcription	Pancreas	Pancrea
5	chr17:34137600-34141200	Weak transcription	Aorta	Aorta
6	chr17:34137600-34143400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:34137600-34149200	Weak transcription	Gastric	stomach
8	chr17:34137800-34139000	Weak transcription	Spleen	Spleen
9	chr17:34137800-34139200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
10	chr17:34137800-34139200	Weak transcription	Lung	lung
11	chr17:34137800-34139200	Transcr. at gene 5' and 3'	A549	lung
12	chr17:34137800-34139400	Enhancers	Primary B cells from peripheral blood	blood
13	chr17:34137800-34139400	Enhancers	Liver	Liver
14	chr17:34137800-34139800	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr17:34137800-34142800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr17:34137800-34142800	Weak transcription	Placenta	Placenta
17	chr17:34137800-34143600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:34137800-34143800	Weak transcription	Left Ventricle	heart
19	chr17:34137800-34144800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:34137800-34145000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:34137800-34149200	Weak transcription	Esophagus	oesophagus
22	chr17:34137800-34149800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:34137800-34152000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr17:34137800-34154000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:34138000-34139000	Enhancers	Primary B cells from cord blood	blood
26	chr17:34138000-34139000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr17:34138000-34139000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr17:34138000-34139200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr17:34138000-34139200	Enhancers	Fetal Kidney	kidney
30	chr17:34138000-34139400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
31	chr17:34138000-34139400	Enhancers	Brain Hippocampus Middle	brain
32	chr17:34138000-34139600	Enhancers	Brain Cingulate Gyrus	brain
33	chr17:34138000-34140000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:34138000-34140200	Weak transcription	Stomach Mucosa	stomach
35	chr17:34138000-34140600	Weak transcription	Fetal Intestine Small	intestine
36	chr17:34138000-34141600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr17:34138000-34143000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:34138000-34143000	Weak transcription	Fetal Muscle Leg	muscle
39	chr17:34138000-34144800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:34138000-34144800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr17:34138000-34145200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr17:34138000-34146200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr17:34138000-34146800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr17:34138000-34149600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr17:34138000-34153400	Weak transcription	Right Ventricle	heart
46	chr17:34138000-34164200	Weak transcription	Colonic Mucosa	Colon
47	chr17:34138200-34139000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:34138200-34139000	Enhancers	Brain Anterior Caudate	brain
49	chr17:34138200-34139000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr17:34138200-34139000	Genic enhancers	Hela-S3	cervix

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