Variant report

Variant	rs11871113
Chromosome Location	chr17:34257559-34257560
allele	G/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	YY1	chr17:34257428-34257950	GM12892	blood:	n/a	n/a
2	YY1	chr17:34257530-34257951	GM12878	blood:	n/a	n/a
3	E2F6	chr17:34257466-34257938	K562	blood:	n/a	chr17:34257776-34257785
4	GTF2F1	chr17:34257550-34258011	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:34257545-34258139	K562	blood:	n/a	n/a
6	POLR2A	chr17:34257458-34257959	MCF-7	breast:	n/a	n/a
7	POLR2A	chr17:34257518-34257850	GM12878	blood:	n/a	n/a
8	E2F4	chr17:34257473-34258524	MCF10A-Er-Src	breast:	n/a	chr17:34257776-34257785
9	YY1	chr17:34257505-34257906	ECC-1	luminal epithelium:	n/a	n/a
10	CHD2	chr17:34257548-34258043	GM12878	blood:	n/a	n/a
11	E2F6	chr17:34257514-34258039	H1-hESC	embryonic stem cell:	n/a	chr17:34257776-34257785
12	E2F6	chr17:34257064-34258140	H1-hESC	embryonic stem cell:	n/a	chr17:34257776-34257785
13	POLR2A	chr17:34257349-34258087	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr17:34257348-34258295	U87	brain:	n/a	n/a
15	E2F6	chr17:34257251-34258015	K562	blood:	n/a	chr17:34257776-34257785
16	POLR2A	chr17:34257481-34258179	H1-hESC	embryonic stem cell:	n/a	n/a
17	SETDB1	chr17:34257550-34258191	U2OS	brain:	n/a	chr17:34257776-34257785
18	IRF1	chr17:34257491-34258130	K562	blood:	n/a	chr17:34257823-34257837
19	POLR2A	chr17:34257394-34258112	GM12892	blood:	n/a	n/a
20	POLR2A	chr17:34257525-34257798	A549	lung:	n/a	n/a
21	ATF3	chr17:34257493-34258046	A549	lung:	n/a	n/a
22	UBTF	chr17:34257368-34258164	K562	blood:	n/a	n/a
23	POLR2A	chr17:34257432-34258140	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr17:34257549-34257803	GM12892	blood:	n/a	n/a
25	POLR2A	chr17:34257323-34258121	GM12891	blood:	n/a	n/a
26	MXI1	chr17:34257425-34258136	GM12878	blood:	n/a	n/a
27	PAX5	chr17:34257541-34258049	GM12878	blood:	n/a	n/a
28	POLR2A	chr17:34257524-34258063	GM18951	blood:	n/a	n/a
29	REST	chr17:34257163-34257967	A549	lung:	n/a	n/a
30	POLR2A	chr17:34257496-34258058	K562	blood:	n/a	n/a
31	TAF1	chr17:34257559-34258080	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr17:34257212-34259498	K562	blood:	n/a	n/a
33	TBL1XR1	chr17:34257552-34258291	K562	blood:	n/a	n/a
34	POLR2A	chr17:34257540-34258143	K562	blood:	n/a	n/a
35	POLR2A	chr17:34257465-34257968	GM12892	blood:	n/a	n/a
36	NRF1	chr17:34257508-34257984	H1-hESC	embryonic stem cell:	n/a	chr17:34257775-34257786 chr17:34257777-34257786 chr17:34257743-34257754 chr17:34257814-34257823 chr17:34257772-34257786 chr17:34257775-34257789 chr17:34257775-34257786
37	BCLAF1	chr17:34257426-34257998	GM12878	blood:	n/a	n/a
38	MAX	chr17:34257441-34258132	ECC-1	luminal epithelium:	n/a	n/a
39	MTA3	chr17:34257282-34258165	GM12878	blood:	n/a	n/a
40	TCF12	chr17:34257504-34257857	GM12878	blood:	n/a	chr17:34257742-34257749
41	POLR2A	chr17:34257503-34257965	A549	lung:	n/a	n/a
42	MAX	chr17:34257403-34258174	A549	lung:	n/a	n/a
43	RFX5	chr17:34257408-34257960	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr17:34257540-34257854	ProgFib	skin:	n/a	n/a
45	SIN3A	chr17:34257356-34258043	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr17:34257513-34257994	GM12878	blood:	n/a	n/a
47	POLR2A	chr17:34257468-34258143	SK-N-SH	brain:	n/a	n/a
48	RCOR1	chr17:34257122-34258087	K562	blood:	n/a	n/a
49	CBX3	chr17:34257536-34258177	K562	blood:	n/a	n/a
50	ZNF384	chr17:34257531-34258256	K562	blood:	n/a	n/a

Variant related genes	Relation type
RDM1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11080363	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11650409	0.82[CEU][hapmap]
rs11653051	0.82[CEU][hapmap]
rs11653282	0.82[CEU][hapmap]
rs11655533	0.82[CEU][hapmap]
rs11657908	0.82[CEU][hapmap]
rs3785764	0.82[CEU][hapmap]
rs4796108	0.82[CEU][hapmap]
rs8064395	0.82[CEU][hapmap]
rs9899866	0.82[CEU][hapmap]
rs9899870	0.82[CEU][hapmap]
rs9900236	0.82[CEU][hapmap]
rs9904675	0.82[CEU][hapmap]
rs9907295	0.82[CEU][hapmap]
rs9908011	0.82[CEU][hapmap]
rs9912284	0.82[CEU][hapmap]
rs9912571	0.82[CEU][hapmap]
rs9913488	0.82[CEU][hapmap]

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	esv3380735	chr17:34246253-34271932	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1063100	chr17:34246253-34397598	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv833424	chr17:34246253-34419476	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1056950	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1059795	chr17:34246253-34442620	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1060457	chr17:34246253-34442620	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv543320	chr17:34246253-34442620	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv949160	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11871113	TAF15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34256800-34258000	Flanking Active TSS	Fetal Thymus	thymus
2	chr17:34257000-34257600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr17:34257000-34257600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr17:34257000-34257600	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr17:34257000-34257600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr17:34257000-34257600	Active TSS	Brain Angular Gyrus	brain
7	chr17:34257000-34257600	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
8	chr17:34257000-34257600	Flanking Active TSS	Colonic Mucosa	Colon
9	chr17:34257000-34257600	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr17:34257000-34257600	Flanking Active TSS	NHEK	skin
11	chr17:34257000-34257800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr17:34257000-34257800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:34257000-34257800	Enhancers	Lung	lung
14	chr17:34257000-34258000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr17:34257000-34258000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr17:34257000-34258000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:34257000-34258000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:34257000-34258000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr17:34257000-34258000	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr17:34257000-34258000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr17:34257000-34258000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:34257000-34258000	Enhancers	Colon Smooth Muscle	Colon
23	chr17:34257000-34258000	Active TSS	Fetal Intestine Large	intestine
24	chr17:34257000-34258000	Active TSS	Fetal Kidney	kidney
25	chr17:34257000-34258000	Flanking Active TSS	Fetal Stomach	stomach
26	chr17:34257000-34258000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr17:34257000-34258000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr17:34257000-34258000	Active TSS	Rectal Smooth Muscle	rectum
29	chr17:34257000-34258000	Flanking Active TSS	HMEC	breast
30	chr17:34257000-34258200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:34257000-34258200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr17:34257000-34258200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:34257000-34258200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:34257000-34258200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr17:34257000-34258200	Flanking Active TSS	Osteobl	bone
36	chr17:34257200-34257600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:34257200-34257600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:34257200-34257600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr17:34257200-34257600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:34257200-34257600	Active TSS	Aorta	Aorta
41	chr17:34257200-34257600	Flanking Active TSS	Fetal Brain Female	brain
42	chr17:34257200-34257600	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr17:34257200-34257600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
44	chr17:34257200-34257600	Flanking Active TSS	Hela-S3	cervix
45	chr17:34257200-34257800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr17:34257200-34257800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr17:34257200-34257800	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr17:34257200-34257800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:34257200-34257800	Enhancers	Spleen	Spleen
50	chr17:34257200-34257800	Active TSS	GM12878-XiMat	blood

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