Variant report

Variant	rs17165709
Chromosome Location	chr7:12250331-12250332
allele	C/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	POLR2A	chr7:12250224-12251340	K562	blood:	n/a	n/a
2	MXI1	chr7:12250092-12251432	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:12250226-12251452	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr7:12249761-12251069	T-47D	breast:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
5	MXI1	chr7:12250104-12251573	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr7:12250318-12251547	K562	blood:	n/a	n/a
7	POLR2A	chr7:12249858-12251921	Hela-S3	cervix:	n/a	n/a
8	NRF1	chr7:12249916-12251408	SK-N-SH	brain:	n/a	chr7:12250843-12250854 chr7:12250843-12250857 chr7:12250840-12250854 chr7:12250842-12250853 chr7:12250843-12250852
9	PML	chr7:12250240-12251378	GM12878	blood:	n/a	n/a
10	TCF7L2	chr7:12250148-12250925	MCF-7	breast:	n/a	chr7:12250703-12250713
11	CREB1	chr7:12250258-12251492	HepG2	liver:	n/a	n/a
12	TFAP2C	chr7:12250167-12251414	Hela-S3	cervix:	n/a	n/a
13	MAX	chr7:12250237-12251538	H1-hESC	embryonic stem cell:	n/a	chr7:12250959-12250969
14	SETDB1	chr7:12250229-12251279	K562	blood:	n/a	chr7:12250844-12250853
15	TCF12	chr7:12250314-12251626	ECC-1	luminal epithelium:	n/a	n/a
16	KAP1	chr7:12250060-12252083	HEK293	kidney:	n/a	chr7:12251695-12251703
17	CHD2	chr7:12250270-12251344	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr7:12250226-12251600	ECC-1	luminal epithelium:	n/a	chr7:12250959-12250969
19	POLR2A	chr7:12250320-12251367	ECC-1	luminal epithelium:	n/a	n/a
20	MAZ	chr7:12250115-12251458	Hela-S3	cervix:	n/a	chr7:12250959-12250969
21	TCF7L2	chr7:12250014-12251353	HCT-116	colon:	n/a	chr7:12250703-12250713
22	KAP1	chr7:12250241-12251500	U2OS	brain:	n/a	n/a
23	BRCA1	chr7:12249731-12251347	Hela-S3	cervix:	n/a	n/a
24	WRNIP1	chr7:12250211-12250915	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:12250257-12251348	GM18951	blood:	n/a	n/a
26	RAD21	chr7:12250059-12251501	Hela-S3	cervix:	n/a	chr7:12251143-12251156
27	RCOR1	chr7:12250242-12251344	GM12878	blood:	n/a	n/a
28	POLR2A	chr7:12250027-12251186	GM12878	blood:	n/a	n/a
29	MTA3	chr7:12250089-12251388	GM12878	blood:	n/a	n/a
30	MAX	chr7:12250126-12251623	ECC-1	luminal epithelium:	n/a	chr7:12250959-12250969
31	MAX	chr7:12250120-12251589	HCT-116	colon:	n/a	chr7:12250959-12250969
32	POLR2A	chr7:12250284-12251417	NB4	blood:	n/a	n/a
33	MAX	chr7:12250222-12251470	GM12878	blood:	n/a	chr7:12250959-12250969
34	POLR2A	chr7:12249931-12252000	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr7:12250105-12252087	GM12878	blood:	n/a	n/a
36	SMC3	chr7:12250082-12251488	Hela-S3	cervix:	n/a	n/a
37	TCF12	chr7:12250007-12251613	A549	lung:	n/a	n/a
38	GATA3	chr7:12249937-12251447	T-47D	breast:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
39	MAZ	chr7:12250229-12251594	GM12878	blood:	n/a	chr7:12250959-12250969
40	MAX	chr7:12250298-12251457	A549	lung:	n/a	chr7:12250959-12250969
41	TAF1	chr7:12250180-12251479	H1-hESC	embryonic stem cell:	n/a	n/a
42	TBP	chr7:12249886-12251545	Hela-S3	cervix:	n/a	n/a
43	GTF2F1	chr7:12250116-12252018	Hela-S3	cervix:	n/a	n/a
44	ATF1	chr7:12250299-12251081	K562	blood:	n/a	n/a
45	BCL3	chr7:12250193-12251334	A549	lung:	n/a	n/a
46	POLR2A	chr7:12250329-12251305	A549	lung:	n/a	n/a
47	EP300	chr7:12250172-12251270	A549	lung:	n/a	chr7:12250633-12250642 chr7:12250927-12250936
48	MAX	chr7:12250116-12251589	HCT-116	colon:	n/a	chr7:12250959-12250969
49	POLR2A	chr7:12250141-12251419	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr7:12250146-12251456	H1-hESC	embryonic stem cell:	n/a	chr7:12251143-12251156

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:12250308-12250358	NT2-D1	testis:	n/a
2	chr7:12250308-12250358	HNPCEpiC	eye:	n/a
3	chr7:12250308-12250358	HCF	heart:	n/a
4	chr7:12250308-12250358	HRCEpiC	kidney:	n/a
5	chr7:12250308-12250358	NHDF-neo	bronchial:	n/a
6	chr7:12250308-12250358	MCF10A-Er-Src	breast:	n/a
7	chr7:12250308-12250358	AG04449	skin:	fetal
8	chr7:12250308-12250358	T-47D	breast:	n/a
9	chr7:12250308-12250358	BE2_C	brain:	n/a
10	chr7:12250308-12250358	AG09319	gingival:	n/a
11	chr7:12250308-12250358	HAEpiC	amniotic membrane:	n/a
12	chr7:12250308-12250358	SK-N-MC	brain:	n/a
13	chr7:12250308-12250358	GM12892	blood:	n/a
14	chr7:12250308-12250358	GM12878	blood:	n/a
15	chr7:12250308-12250358	AoSMC	blood vessel:	n/a
16	chr7:12250308-12250358	GM12891	blood:	n/a
17	chr7:12250308-12250358	HMEC	breast:	n/a
18	chr7:12250308-12250358	HRE	kidney:	n/a
19	chr7:12250308-12250358	HL-60	blood:	n/a
20	chr7:12250308-12250358	LNCaP	prostate:	n/a
21	chr7:12250308-12250358	PANC-1	pancreas:	n/a
22	chr7:12250308-12250358	RPTEC	kidney:	n/a
23	chr7:12250308-12250358	GM19239	blood:	n/a
24	chr7:12250308-12250358	HCT-116	colon:	n/a
25	chr7:12250308-12250358	HIPEpiC	eye:	n/a
26	chr7:12250308-12250358	HepG2	liver:	n/a
27	chr7:12250308-12250358	HEK293	kidney:	embryo
28	chr7:12250308-12250358	Caco-2	colon:	n/a
29	chr7:12250308-12250358	IMR90	lung:	fetal
30	chr7:12250308-12250358	HCPEpiC	choroid plexus:	n/a
31	chr7:12250308-12250358	NHBE	bronchial:	n/a
32	chr7:12250308-12250358	ovcar-3	ovarian:	n/a
33	chr7:12250308-12250358	SK-N-SH_RA	brain:	n/a
34	chr7:12250308-12250358	K562	blood:	n/a
35	chr7:12250308-12250358	HEEpiC	esophagus:	n/a
36	chr7:12250308-12250358	SK-N-SH	brain:	n/a
37	chr7:12250308-12250358	AG04450	lung:	fetal
38	chr7:12250308-12250358	Hepatocyte	liver:	n/a
39	chr7:12250308-12250358	HCM	heart:	n/a
40	chr7:12250308-12250358	CMK	blood:	n/a
41	chr7:12250308-12250358	AG09309	skin:	n/a
42	chr7:12250308-12250358	MCF-7	breast:	n/a
43	chr7:12250308-12250358	HUVEC	blood vessel:	n/a
44	chr7:12250308-12250358	Jurkat	blood:	n/a
45	chr7:12250308-12250358	ECC-1	luminal epithelium:	n/a
46	chr7:12250308-12250358	GM06990	blood:	n/a
47	chr7:12250308-12250358	BJ	skin:	n/a
48	chr7:12250308-12250358	PrEC	prostate:	n/a
49	chr7:12250308-12250358	SKMC	muscle:	n/a
50	chr7:12250308-12250358	AG10803	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12248340..12250610-chr7:12341759..12344659,2	K562	blood:
2	chr20:44563231..44563776-chr7:12249962..12250824,2	Hela-S3	cervix:
3	chr7:12245428..12248475-chr7:12248558..12250664,3	K562	blood:
4	chr7:12237815..12240381-chr7:12248250..12250812,3	K562	blood:

Variant related genes	Relation type
TMEM106B	TF binding region
TMEM106B	CpG island
ENSG00000100982	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10262993	1.00[EUR][1000 genomes]
rs10263331	1.00[EUR][1000 genomes]
rs10266698	1.00[EUR][1000 genomes]
rs10274501	1.00[EUR][1000 genomes]
rs1072262	1.00[EUR][1000 genomes]
rs1595012	1.00[EUR][1000 genomes]
rs16877307	1.00[EUR][1000 genomes]
rs17165685	1.00[EUR][1000 genomes]
rs17165707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28471043	1.00[EUR][1000 genomes]
rs57209188	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57259822	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57308211	1.00[EUR][1000 genomes]
rs57698857	1.00[EUR][1000 genomes]
rs57742006	1.00[EUR][1000 genomes]
rs57812376	1.00[EUR][1000 genomes]
rs58476665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58749049	1.00[EUR][1000 genomes]
rs58818488	1.00[EUR][1000 genomes]
rs58954316	1.00[EUR][1000 genomes]
rs59080097	1.00[EUR][1000 genomes]
rs59769625	1.00[EUR][1000 genomes]
rs60817474	1.00[EUR][1000 genomes]
rs61411483	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6947477	1.00[EUR][1000 genomes]
rs6977974	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6978326	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73289387	1.00[EUR][1000 genomes]
rs73290454	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73291081	1.00[EUR][1000 genomes]
rs73291082	1.00[EUR][1000 genomes]
rs73292961	1.00[EUR][1000 genomes]
rs73292962	1.00[EUR][1000 genomes]
rs73292964	1.00[EUR][1000 genomes]
rs73292965	1.00[EUR][1000 genomes]
rs73295078	1.00[EUR][1000 genomes]
rs73296310	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73297023	1.00[EUR][1000 genomes]
rs73297098	1.00[EUR][1000 genomes]
rs73301022	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73301040	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73679942	1.00[EUR][1000 genomes]
rs7786770	1.00[EUR][1000 genomes]
rs7786784	1.00[EUR][1000 genomes]
rs7801599	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
3	nsv1021710	chr7:12164993-12251790	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12249600-12250400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:12249600-12250400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr7:12249600-12250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:12249800-12250400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:12249800-12250400	Flanking Active TSS	Fetal Brain Male	brain
6	chr7:12249800-12250400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
7	chr7:12249800-12250400	Active TSS	K562	blood
8	chr7:12249800-12250600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr7:12249800-12250600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr7:12249800-12250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:12249800-12250800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr7:12249800-12251000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr7:12249800-12251200	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr7:12249800-12251400	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr7:12249800-12251400	Active TSS	Fetal Brain Female	brain
16	chr7:12249800-12251600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:12249800-12251600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr7:12249800-12251600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr7:12249800-12251600	Active TSS	Brain Angular Gyrus	brain
20	chr7:12249800-12251600	Active TSS	Brain Substantia Nigra	brain
21	chr7:12249800-12251600	Active TSS	Duodenum Mucosa	Duodenum
22	chr7:12249800-12251600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr7:12249800-12251600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr7:12249800-12251600	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr7:12249800-12251600	Active TSS	Stomach Smooth Muscle	stomach
26	chr7:12249800-12251600	Active TSS	NH-A	brain
27	chr7:12249800-12251800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:12249800-12251800	Active TSS	Brain Cingulate Gyrus	brain
29	chr7:12249800-12251800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:12249800-12252000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:12249800-12252200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:12249800-12252200	Active TSS	Right Atrium	heart
33	chr7:12249800-12253000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr7:12250000-12250400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:12250000-12250400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr7:12250000-12250400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
37	chr7:12250000-12250400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr7:12250000-12250400	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr7:12250000-12250400	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr7:12250000-12250400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr7:12250000-12250400	Flanking Active TSS	HMEC	breast
42	chr7:12250000-12250400	Flanking Active TSS	Osteobl	bone
43	chr7:12250000-12251000	Active TSS	Primary T cells fromperipheralblood	blood
44	chr7:12250000-12251200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:12250000-12251200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:12250000-12251400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr7:12250000-12251400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:12250000-12251600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:12250000-12251600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:12250000-12251600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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