Variant report

Variant	rs66652835
Chromosome Location	chr17:46177840-46177841
allele	A/G
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	HCFC1	chr17:46177573-46179332	Hela-S3	cervix:	n/a	n/a
2	TEAD4	chr17:46177602-46178235	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:46177811-46179231	HUVEC	blood vessel:	n/a	n/a
4	MAX	chr17:46177773-46179228	HepG2	liver:	n/a	chr17:46178416-46178426
5	POLR2A	chr17:46177775-46177966	MCF10A-Er-Src	breast:	n/a	n/a
6	SIN3A	chr17:46177794-46179144	H1-hESC	embryonic stem cell:	n/a	chr17:46178012-46178020
7	POLR2A	chr17:46177794-46178274	Hela-S3	cervix:	n/a	n/a
8	MAX	chr17:46177667-46179113	ECC-1	luminal epithelium:	n/a	chr17:46178416-46178426
9	MTA3	chr17:46177637-46179216	GM12878	blood:	n/a	n/a
10	MAZ	chr17:46177804-46179065	HepG2	liver:	n/a	chr17:46178416-46178426
11	TCF12	chr17:46177473-46179282	A549	lung:	n/a	chr17:46178440-46178447
12	MAX	chr17:46177529-46179313	HCT-116	colon:	n/a	chr17:46178416-46178426
13	POLR2A	chr17:46177810-46179092	H1-neurons	neurons:	n/a	n/a
14	ZNF263	chr17:46177755-46179056	HEK293-T-REx	kidney:	n/a	chr17:46178015-46178024 chr17:46178084-46178105 chr17:46178143-46178164
15	BRCA1	chr17:46177753-46178156	HepG2	liver:	n/a	n/a
16	ZNF384	chr17:46177519-46178048	K562	blood:	n/a	n/a
17	MAX	chr17:46177829-46179112	MCF-7	breast:	n/a	chr17:46178416-46178426
18	SIN3AK20	chr17:46177477-46179256	MCF-7	breast:	n/a	n/a
19	POLR2A	chr17:46177788-46179218	HCT-116	colon:	n/a	n/a
20	SIX5	chr17:46177546-46179423	A549	lung:	n/a	n/a
21	FOS	chr17:46177541-46178118	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr17:46177705-46179092	H1-neurons	neurons:	n/a	n/a
23	STAT3	chr17:46177587-46178068	MCF10A-Er-Src	breast:	n/a	chr17:46178048-46178060
24	REST	chr17:46177476-46179373	H1-neurons	neurons:	n/a	chr17:46178509-46178522 chr17:46177721-46177741 chr17:46178416-46178429 chr17:46178602-46178615 chr17:46178052-46178065 chr17:46178161-46178175 chr17:46178832-46178845
25	MYC	chr17:46177589-46178142	MCF10A-Er-Src	breast:	n/a	n/a
26	REST	chr17:46177778-46179135	A549	lung:	n/a	chr17:46178509-46178522 chr17:46178416-46178429 chr17:46178602-46178615 chr17:46178052-46178065 chr17:46178161-46178175 chr17:46178832-46178845
27	MAX	chr17:46177816-46179132	SK-N-SH	brain:	n/a	chr17:46178416-46178426
28	MAX	chr17:46177721-46179315	A549	lung:	n/a	chr17:46178416-46178426
29	FOSL2	chr17:46177786-46178675	A549	lung:	n/a	n/a
30	POLR2A	chr17:46177641-46179310	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr17:46177794-46179122	H1-hESC	embryonic stem cell:	n/a	n/a
32	RCOR1	chr17:46177722-46179060	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr17:46177566-46178235	Hela-S3	cervix:	n/a	n/a
34	MAX	chr17:46177812-46179132	ECC-1	luminal epithelium:	n/a	chr17:46178416-46178426
35	SIN3AK20	chr17:46177798-46179351	SK-N-SH	brain:	n/a	n/a
36	MAX	chr17:46177800-46179109	SK-N-SH	brain:	n/a	chr17:46178416-46178426
37	POLR2A	chr17:46177604-46179246	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr17:46177633-46178998	IMR90	lung:	n/a	n/a
39	POLR2A	chr17:46177822-46179283	PANC-1	pancreas:	n/a	n/a
40	CEBPB	chr17:46177528-46178164	IMR90	lung:	n/a	n/a
41	WRNIP1	chr17:46177634-46178246	GM12878	blood:	n/a	n/a
42	MBD4	chr17:46177648-46178390	HepG2	liver:	n/a	n/a
43	TCF12	chr17:46177798-46179063	ECC-1	luminal epithelium:	n/a	chr17:46178440-46178447
44	CEBPB	chr17:46177601-46178183	A549	lung:	n/a	n/a
45	TCF12	chr17:46177729-46179325	ECC-1	luminal epithelium:	n/a	chr17:46178440-46178447
46	SP1	chr17:46177763-46179313	A549	lung:	n/a	chr17:46178605-46178619 chr17:46178052-46178061 chr17:46178416-46178426 chr17:46178417-46178426 chr17:46178416-46178425 chr17:46178052-46178066 chr17:46178051-46178063 chr17:46178051-46178063 chr17:46178416-46178430 chr17:46178699-46178709 chr17:46178415-46178427 chr17:46178053-46178062 chr17:46178415-46178427 chr17:46178699-46178709 chr17:46178052-46178062
47	POLR2A	chr17:46177720-46179149	ECC-1	luminal epithelium:	n/a	n/a
48	E2F4	chr17:46177660-46177963	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr17:46177557-46177913	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
2	chr17:46177274..46179922-chr17:46706362..46708559,2	K562	blood:
3	chr17:46125418..46126971-chr17:46177352..46179960,2	K562	blood:
4	chr17:46124025..46127922-chr17:46176725..46180326,7	MCF-7	breast:
5	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:
6	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
7	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
8	chr17:46177349..46182213-chr17:46183318..46186399,5	K562	blood:
9	chr17:46177349..46180853-chr17:46182060..46186447,10	K562	blood:

Variant related genes	Relation type
SNX11	TF binding region
ENSG00000263412	Chromatin interaction
ENSG00000242207	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12373126	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3805364	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3805366	0.81[ASN][1000 genomes]
rs3805368	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56937221	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59493350	0.80[AMR][1000 genomes]
rs61197535	0.80[AMR][1000 genomes]
rs66479254	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66490008	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66727366	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66727715	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66743695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66753385	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66950931	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67162925	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67230974	0.86[EUR][1000 genomes]
rs67275838	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67307876	0.93[EUR][1000 genomes]
rs67412675	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67647500	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67847113	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs67940055	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67991353	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68092669	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68144131	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72825550	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72825592	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73320817	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73320825	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73324737	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73327306	0.80[AMR][1000 genomes]
rs73332969	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 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	chr17:46149000-46178000	Weak transcription	Lung	lung
2	chr17:46175000-46178000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:46176800-46178000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr17:46176800-46178200	Flanking Active TSS	Brain Germinal Matrix	brain
5	chr17:46176800-46179400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr17:46177000-46178000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr17:46177000-46178200	Flanking Active TSS	GM12878-XiMat	blood
8	chr17:46177000-46179400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr17:46177000-46179400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr17:46177000-46179400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr17:46177000-46179600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr17:46177200-46178000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr17:46177200-46178000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr17:46177200-46178000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:46177200-46178600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:46177200-46179200	Active TSS	HSMM	muscle
17	chr17:46177200-46179400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr17:46177200-46179400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:46177200-46179400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:46177200-46179400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:46177200-46179400	Active TSS	K562	blood
22	chr17:46177200-46179600	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr17:46177200-46179600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr17:46177200-46179600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:46177200-46179600	Active TSS	NHLF	lung
26	chr17:46177400-46178000	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr17:46177400-46178000	Flanking Active TSS	HUVEC	blood vessel
28	chr17:46177400-46179200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr17:46177400-46179200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:46177400-46179200	Active TSS	NHEK	skin
31	chr17:46177400-46179400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr17:46177400-46179400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr17:46177400-46179400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:46177400-46179400	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr17:46177400-46179400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:46177400-46179400	Active TSS	HMEC	breast
37	chr17:46177400-46179600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:46177400-46179600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:46177600-46178000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr17:46177600-46178000	Enhancers	Primary B cells from peripheral blood	blood
41	chr17:46177600-46178000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr17:46177600-46178000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:46177600-46178000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr17:46177600-46178000	Flanking Active TSS	Brain Cingulate Gyrus	brain
45	chr17:46177600-46178000	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr17:46177600-46178000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr17:46177600-46178000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr17:46177600-46178000	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr17:46177600-46178000	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr17:46177600-46178000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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