Variant report

Variant	rs17163792
Chromosome Location	chr7:10979072-10979073
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr7:10978925-10979463	HepG2	liver:	n/a	n/a
2	MAX	chr7:10979040-10979265	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr7:10978837-10980899	SK-N-MC	brain:	n/a	n/a
4	SIN3A	chr7:10978945-10980461	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:10979039-10980471	K562	blood:	n/a	n/a
6	FOXM1	chr7:10979019-10980712	GM12878	blood:	n/a	n/a
7	MYBL2	chr7:10979031-10980498	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:10978928-10980584	Hela-S3	cervix:	n/a	n/a
9	MAX	chr7:10979035-10980484	Hela-S3	cervix:	n/a	n/a
10	CEBPB	chr7:10979027-10979228	H1-hESC	embryonic stem cell:	n/a	n/a
11	FOXA1	chr7:10978970-10979419	HepG2	liver:	n/a	n/a
12	TAF1	chr7:10979044-10980427	K562	blood:	n/a	n/a
13	SMARCC2	chr7:10979022-10980952	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr7:10978943-10980975	GM19099	blood:	n/a	n/a
15	USF2	chr7:10979058-10979157	GM12878	blood:	n/a	n/a
16	GATA1	chr7:10978403-10980484	PBDE	blood:	n/a	n/a
17	POLR2A	chr7:10979024-10980544	K562	blood:	n/a	n/a
18	POLR2A	chr7:10978895-10980973	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr7:10979048-10980445	HepG2	liver:	n/a	n/a
20	WRNIP1	chr7:10979013-10981084	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:10978979-10980423	IMR90	lung:	n/a	n/a
22	EBF1	chr7:10979032-10979332	GM12878	blood:	n/a	n/a
23	MYC	chr7:10979049-10980294	MCF10A-Er-Src	breast:	n/a	n/a
24	MYC	chr7:10978913-10980846	K562	blood:	n/a	chr7:10980620-10980630
25	HCFC1	chr7:10978577-10980749	Hela-S3	cervix:	n/a	n/a
26	FOXA1	chr7:10979056-10979909	HepG2	liver:	n/a	n/a
27	CEBPB	chr7:10978966-10980509	Hela-S3	cervix:	n/a	chr7:10979232-10979243
28	POLR2A	chr7:10978425-10981243	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr7:10978888-10980493	K562	blood:	n/a	n/a
30	RELA	chr7:10979014-10981067	GM18951	blood:	n/a	n/a
31	TBP	chr7:10979032-10980925	K562	blood:	n/a	n/a
32	MYC	chr7:10978983-10980497	NB4	blood:	n/a	n/a
33	POLR2A	chr7:10979051-10980941	HepG2	liver:	n/a	n/a
34	POLR2A	chr7:10978951-10980658	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:10979011-10981217	K562	blood:	n/a	n/a
36	POLR2A	chr7:10979012-10980790	GM12878	blood:	n/a	n/a
37	CHD1	chr7:10978478-10980573	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr7:10979007-10980829	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr7:10979049-10979376	HCT-116	colon:	n/a	n/a
40	POLR2A	chr7:10978593-10980990	PBDE	blood:	n/a	n/a
41	MAX	chr7:10978929-10981089	NB4	blood:	n/a	chr7:10980620-10980630
42	RCOR1	chr7:10978927-10981017	IMR90	lung:	n/a	n/a
43	GTF2F1	chr7:10979028-10980483	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr7:10979000-10981606	GM12891	blood:	n/a	n/a
45	REST	chr7:10979024-10980738	H1-neurons	neurons:	n/a	chr7:10980456-10980469 chr7:10980190-10980203
46	POLR2A	chr7:10978937-10980936	MCF10A-Er-Src	breast:	n/a	n/a
47	MBD4	chr7:10979070-10980188	HepG2	liver:	n/a	n/a
48	RFX5	chr7:10978962-10980408	Hela-S3	cervix:	n/a	n/a
49	MAX	chr7:10979000-10980669	A549	lung:	n/a	chr7:10980620-10980630
50	POLR2A	chr7:10979006-10980604	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:10978101..10982429-chr7:11011509..11017731,20	K562	blood:
2	chr7:10976808..10978708-chr7:10978899..10981503,2	MCF-7	breast:
3	chr7:10975906..10982429-chr7:11007978..11018673,26	K562	blood:
4	chr7:10977305..10982144-chr7:11011875..11016071,10	MCF-7	breast:
5	chr7:10978242..10981238-chr7:11011671..11015550,7	MCF-7	breast:
6	chr7:10978313..10981160-chr7:11099563..11101890,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271185	TF binding region
NDUFA4	TF binding region
ENSG00000106443	Chromatin interaction
ENSG00000189043	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10272132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532975	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533265	1.00[ASN][1000 genomes]
rs12537541	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12539905	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540053	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12540752	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17163781	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163788	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17163795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73678313	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067780	chr7:10649696-11329787	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv491695	chr7:10649696-11329787	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1018905	chr7:10679889-10980691	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv532092	chr7:10731350-11414759	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv887600	chr7:10807685-11090546	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	nsv949387	chr7:10815994-11281536	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	esv2752140	chr7:10817060-11029748	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv1029882	chr7:10872162-11371145	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv817291	chr7:10875417-11562683	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv1031498	chr7:10882696-11110412	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv464364	chr7:10904752-10988866	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv606193	chr7:10904752-10988866	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv887601	chr7:10912949-11049523	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv1027289	chr7:10976057-10992462	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17163792	RND3	trans	lymphoblastoid	seeQTL
rs17163792	TOX3	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:10971200-10979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:10977000-10980800	Active TSS	Aorta	Aorta
3	chr7:10977400-10979200	Weak transcription	Spleen	Spleen
4	chr7:10977400-10980800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr7:10977400-10980800	Active TSS	Right Atrium	heart
6	chr7:10977600-10981000	Active TSS	GM12878-XiMat	blood
7	chr7:10977800-10980800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr7:10977800-10980800	Active TSS	Right Ventricle	heart
9	chr7:10978000-10979600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:10978000-10980600	Active TSS	A549	lung
11	chr7:10978000-10980800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr7:10978000-10980800	Active TSS	Psoas Muscle	Psoas
13	chr7:10978200-10979200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr7:10978200-10979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:10978200-10979400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:10978200-10980400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:10978200-10980400	Active TSS	NHLF	lung
18	chr7:10978200-10980600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:10978200-10980600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:10978200-10980600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr7:10978200-10980600	Active TSS	Fetal Stomach	stomach
22	chr7:10978200-10980600	Active TSS	HSMM	muscle
23	chr7:10978200-10980800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:10978200-10980800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:10978200-10980800	Active TSS	Fetal Intestine Small	intestine
26	chr7:10978200-10980800	Active TSS	Fetal Kidney	kidney
27	chr7:10978200-10980800	Active TSS	Ovary	ovary
28	chr7:10978200-10980800	Active TSS	HSMMtube	muscle
29	chr7:10978200-10981000	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr7:10978200-10981000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:10978200-10981000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:10978200-10981000	Active TSS	Stomach Smooth Muscle	stomach
33	chr7:10978200-10981200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr7:10978400-10979200	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr7:10978400-10979200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:10978400-10979200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr7:10978400-10979200	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr7:10978400-10979400	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr7:10978400-10979400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr7:10978400-10979600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr7:10978400-10979800	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr7:10978400-10980600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr7:10978400-10980600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:10978400-10980600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:10978400-10980600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:10978400-10980600	Active TSS	Colonic Mucosa	Colon
47	chr7:10978400-10980800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr7:10978400-10980800	Active TSS	Muscle Satellite Cultured Cells	--
49	chr7:10978400-10980800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:10978400-10980800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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