Variant report

Variant	rs7209653
Chromosome Location	chr17:19882084-19882085
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	REST	chr17:19880354-19882109	A549	lung:	n/a	chr17:19881684-19881694
2	POLR2A	chr17:19880115-19882375	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:19880545-19882178	GM19099	blood:	n/a	n/a
4	BHLHE40	chr17:19880952-19882354	GM12878	blood:	n/a	chr17:19881207-19881223
5	MAX	chr17:19880443-19882108	NB4	blood:	n/a	chr17:19880497-19880504 chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251 chr17:19882034-19882043
6	POLR2A	chr17:19879996-19884397	H1-hESC	embryonic stem cell:	n/a	n/a
7	USF1	chr17:19881843-19882158	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr17:19880021-19882329	SK-N-SH	brain:	n/a	chr17:19881243-19881252 chr17:19880842-19880851
9	MTA3	chr17:19880470-19882264	GM12878	blood:	n/a	n/a
10	KAP1	chr17:19881731-19882697	K562	blood:	n/a	n/a
11	POLR2A	chr17:19880471-19882496	Raji	blood:	n/a	n/a
12	SIN3A	chr17:19880415-19882206	H1-hESC	embryonic stem cell:	n/a	chr17:19881098-19881107 chr17:19881243-19881252 chr17:19881893-19881907 chr17:19881241-19881250 chr17:19881924-19881935
13	POLR2A	chr17:19880499-19882629	H1-hESC	embryonic stem cell:	n/a	n/a
14	KAP1	chr17:19881262-19882406	HEK293	kidney:	n/a	n/a
15	SETDB1	chr17:19881200-19882413	U2OS	brain:	n/a	n/a
16	TAF1	chr17:19880465-19882593	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr17:19880342-19882096	GM18505	blood:	n/a	n/a
18	JUND	chr17:19880833-19882175	H1-hESC	embryonic stem cell:	n/a	chr17:19881125-19881134
19	POLR2A	chr17:19880194-19882348	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:19880029-19882113	GM12878	blood:	n/a	n/a
21	POLR2A	chr17:19880562-19882605	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAZ	chr17:19880276-19882177	IMR90	lung:	n/a	chr17:19880497-19880504 chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251 chr17:19882034-19882043
23	POLR2A	chr17:19880559-19882549	H1-hESC	embryonic stem cell:	n/a	n/a
24	EP300	chr17:19881133-19882093	GM12878	blood:	n/a	chr17:19881398-19881414
25	MYC	chr17:19880271-19882177	NB4	blood:	n/a	chr17:19880497-19880504 chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251 chr17:19882034-19882043
26	CTCF	chr17:19881800-19882170	BJ	skin:	n/a	n/a
27	POLR2A	chr17:19880469-19882482	NB4	blood:	n/a	n/a
28	TBP	chr17:19880580-19882522	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD1	chr17:19880264-19882438	H1-hESC	embryonic stem cell:	n/a	chr17:19880440-19880450
30	CBX3	chr17:19881030-19882522	K562	blood:	n/a	n/a
31	POLR2A	chr17:19880472-19882195	GM19193	blood:	n/a	n/a
32	MXI1	chr17:19880719-19882338	H1-hESC	embryonic stem cell:	n/a	chr17:19881243-19881252 chr17:19880842-19880851
33	E2F6	chr17:19880542-19882123	H1-hESC	embryonic stem cell:	n/a	chr17:19881039-19881046 chr17:19881039-19881046 chr17:19881181-19881191 chr17:19880907-19880922 chr17:19881039-19881046 chr17:19880881-19880890 chr17:19880885-19880895
34	MYC	chr17:19881013-19882498	H1-hESC	embryonic stem cell:	n/a	chr17:19881241-19881252 chr17:19881244-19881260 chr17:19881240-19881249 chr17:19881242-19881251 chr17:19882034-19882043
35	TAF7	chr17:19880486-19882529	H1-hESC	embryonic stem cell:	n/a	n/a
36	GTF2F1	chr17:19880949-19882432	H1-hESC	embryonic stem cell:	n/a	n/a
37	SETDB1	chr17:19881019-19882355	K562	blood:	n/a	n/a
38	SPI1	chr17:19881243-19882182	GM12878	blood:	n/a	chr17:19881708-19881721
39	POLR2A	chr17:19880122-19882194	GM12878	blood:	n/a	n/a
40	CBX3	chr17:19882052-19882317	K562	blood:	n/a	n/a
41	HCFC1	chr17:19880022-19882096	Hela-S3	cervix:	n/a	n/a
42	ATF2	chr17:19881613-19882372	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19881500..19882356-chr17:74553533..74554276,2	NB4	blood:
2	chr17:19769754..19773058-chr17:19878983..19882883,4	MCF-7	breast:
3	chr17:19879148..19882537-chr17:19911149..19913260,3	MCF-7	breast:
4	chr17:19874894..19877588-chr17:19882059..19884637,2	MCF-7	breast:
5	chr17:19769588..19772074-chr17:19879592..19882526,4	MCF-7	breast:
6	chr17:19861091..19865827-chr17:19879221..19882528,6	MCF-7	breast:
7	chr17:19878871..19883594-chr17:20057277..20060362,4	K562	blood:
8	chr17:19881019..19882535-chr17:19912703..19915442,2	K562	blood:
9	chr17:19880813..19883681-chr17:19988880..19990706,2	MCF-7	breast:

Variant related genes	Relation type
AKAP10	TF binding region
ENSG00000128487	Chromatin interaction
ENSG00000267546	Chromatin interaction
ENSG00000261033	Chromatin interaction
ENSG00000163597	Chromatin interaction
ENSG00000083290	Chromatin interaction
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11204422	0.89[JPT][hapmap]
rs11867585	0.81[JPT][hapmap]
rs11870381	0.90[JPT][hapmap]
rs12449662	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12450857	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12451841	0.90[JPT][hapmap]
rs12453720	0.95[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12936794	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12942179	0.81[JPT][hapmap]
rs12943369	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12944084	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12947713	0.90[JPT][hapmap]
rs1638526	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1638527	0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1638528	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs169413	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17604987	0.87[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17605101	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17668529	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17686798	0.90[JPT][hapmap]
rs17759609	0.87[CEU][hapmap];0.87[MEX][hapmap]
rs17759959	0.90[JPT][hapmap]
rs203449	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs203454	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203464	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs203467	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs203474	0.86[EUR][1000 genomes]
rs203475	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203476	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs203478	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs203480	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2072337	1.00[JPT][hapmap]
rs2108981	0.95[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28424266	0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs34182788	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34726000	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35254155	0.83[AMR][1000 genomes]
rs35315252	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35925051	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35979784	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36097967	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs403021	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4141185	1.00[JPT][hapmap]
rs427033	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4924808	0.90[JPT][hapmap]
rs4925063	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4925064	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4925075	0.90[JPT][hapmap];0.83[MEX][hapmap]
rs4925082	0.90[JPT][hapmap]
rs56005410	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62066345	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066346	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066347	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62066348	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066349	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066350	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066351	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62066352	0.84[AMR][1000 genomes]
rs6587207	0.90[JPT][hapmap]
rs6813	0.94[ASW][hapmap];0.91[CEU][hapmap];0.96[GIH][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7207459	0.90[JPT][hapmap]
rs7215803	0.90[JPT][hapmap]
rs7224875	0.90[JPT][hapmap]
rs8065122	0.82[ASN][1000 genomes]
rs8068484	0.90[JPT][hapmap]
rs8075343	0.90[JPT][hapmap]
rs8079923	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8080190	0.90[JPT][hapmap]
rs850622	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs888424	0.90[JPT][hapmap]
rs9891503	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9893296	0.86[ASN][1000 genomes]
rs9897653	0.81[JPT][hapmap]
rs9901294	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915039	0.90[JPT][hapmap]
rs9944451	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7209653	AKAP10	cis	Lymphoblastoid	GTEx
rs7209653	AKAP10	cis	multi-tissue	Pritchard
rs7209653	AKAP10	cis	lymphoblastoid	seeQTL
rs7209653	SMCR5	cis	parietal	SCAN
rs7209653	ENSG00000108599	cis	multi-tissue	Pritchard

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19879400-19882400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr17:19880000-19882200	Active TSS	Fetal Lung	lung
3	chr17:19880000-19882400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr17:19880000-19882400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr17:19880000-19884000	Active TSS	H1 Cell Line	embryonic stem cell
6	chr17:19880200-19882400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr17:19880200-19884400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr17:19880400-19882200	Active TSS	Brain Cingulate Gyrus	brain
9	chr17:19880400-19882400	Active TSS	Brain Anterior Caudate	brain
10	chr17:19880400-19882400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr17:19880600-19882400	Active TSS	Brain Angular Gyrus	brain
12	chr17:19880800-19882200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr17:19881200-19882200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr17:19881200-19882400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr17:19881200-19884200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr17:19881400-19882200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr17:19881400-19882200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:19881400-19882400	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr17:19881400-19882400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr17:19881400-19882400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr17:19881400-19882400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr17:19881400-19882400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:19881400-19882400	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr17:19881400-19882400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr17:19881400-19882400	Flanking Active TSS	Dnd41	blood
26	chr17:19881400-19882400	Flanking Active TSS	GM12878-XiMat	blood
27	chr17:19881400-19882600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr17:19881400-19882600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:19881400-19884200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr17:19881400-19884400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:19881600-19882200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:19881600-19882200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:19881600-19882200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr17:19881600-19882200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr17:19881600-19882200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr17:19881600-19882200	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr17:19881600-19882200	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr17:19881600-19882200	Flanking Active TSS	Rectal Smooth Muscle	rectum
39	chr17:19881600-19882200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr17:19881600-19882400	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr17:19881600-19882400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:19881800-19882200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:19881800-19882200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr17:19881800-19882200	Enhancers	Fetal Heart	heart
45	chr17:19881800-19882200	Flanking Active TSS	Right Atrium	heart
46	chr17:19881800-19882200	Enhancers	NHLF	lung
47	chr17:19881800-19882400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:19881800-19882400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr17:19881800-19882400	Enhancers	Esophagus	oesophagus
50	chr17:19881800-19882400	Enhancers	Lung	lung

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