Variant report

Variant	rs17165707
Chromosome Location	chr7:12250023-12250024
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	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
2	POLR2A	chr7:12249858-12251921	Hela-S3	cervix:	n/a	n/a
3	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
4	TCF7L2	chr7:12250014-12251353	HCT-116	colon:	n/a	chr7:12250703-12250713
5	BRCA1	chr7:12249731-12251347	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:12249931-12252000	PANC-1	pancreas:	n/a	n/a
7	TCF12	chr7:12250007-12251613	A549	lung:	n/a	n/a
8	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
9	TBP	chr7:12249886-12251545	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr7:12249912-12251993	Hela-S3	cervix:	n/a	n/a
11	GATA2	chr7:12249808-12252102	SH-SY5Y	brain:	n/a	chr7:12251837-12251848 chr7:12250250-12250260 chr7:12251927-12251936 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12251929-12251939 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12251926-12251938 chr7:12250248-12250258
12	HCFC1	chr7:12249737-12252247	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr7:12249976-12251500	H1-neurons	neurons:	n/a	n/a
14	GATA3	chr7:12249708-12250935	SH-SY5Y	brain:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
15	GATA2	chr7:12249853-12250964	HUVEC	blood vessel:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
16	MAX	chr7:12249992-12251640	A549	lung:	n/a	chr7:12250959-12250969
17	MAFK	chr7:12249915-12251481	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr7:12249817-12252183	MCF10A-Er-Src	breast:	n/a	n/a
19	ZKSCAN1	chr7:12249837-12251913	Hela-S3	cervix:	n/a	n/a
20	GATA3	chr7:12249898-12251417	A549	lung:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
21	RCOR1	chr7:12249922-12251525	Hela-S3	cervix:	n/a	n/a
22	ARID3A	chr7:12250005-12251450	HepG2	liver:	n/a	n/a
23	POLR2A	chr7:12249953-12251981	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr7:12250003-12252077	HepG2	liver:	n/a	n/a
25	POLR2A	chr7:12250005-12252072	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr7:12249858-12251684	PANC-1	pancreas:	n/a	n/a
27	CEBPB	chr7:12249917-12251457	Hela-S3	cervix:	n/a	n/a
28	MAZ	chr7:12249937-12251503	IMR90	lung:	n/a	chr7:12250959-12250969

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
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]
rs17165709	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28471043	1.00[EUR][1000 genomes]
rs57209188	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57259822	0.85[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	1.00[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	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6947477	1.00[EUR][1000 genomes]
rs6977974	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6978326	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73289387	1.00[EUR][1000 genomes]
rs73290454	0.85[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	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73297023	1.00[EUR][1000 genomes]
rs73297098	1.00[EUR][1000 genomes]
rs73301022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73301040	0.87[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:114 , 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	chr7:12249800-12250200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr7:12249800-12250200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr7:12249800-12250200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:12249800-12250200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr7:12249800-12250200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr7:12249800-12250200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr7:12249800-12250200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:12249800-12250200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr7:12249800-12250200	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr7:12249800-12250200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr7:12249800-12250200	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr7:12249800-12250200	Flanking Active TSS	HepG2	liver
16	chr7:12249800-12250200	Flanking Active TSS	HUVEC	blood vessel
17	chr7:12249800-12250200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr7:12249800-12250400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:12249800-12250400	Flanking Active TSS	Fetal Brain Male	brain
20	chr7:12249800-12250400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
21	chr7:12249800-12250400	Active TSS	K562	blood
22	chr7:12249800-12250600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr7:12249800-12250600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr7:12249800-12250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:12249800-12250800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr7:12249800-12251000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:12249800-12251200	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr7:12249800-12251400	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr7:12249800-12251400	Active TSS	Fetal Brain Female	brain
30	chr7:12249800-12251600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:12249800-12251600	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr7:12249800-12251600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:12249800-12251600	Active TSS	Brain Angular Gyrus	brain
34	chr7:12249800-12251600	Active TSS	Brain Substantia Nigra	brain
35	chr7:12249800-12251600	Active TSS	Duodenum Mucosa	Duodenum
36	chr7:12249800-12251600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr7:12249800-12251600	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr7:12249800-12251600	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr7:12249800-12251600	Active TSS	Stomach Smooth Muscle	stomach
40	chr7:12249800-12251600	Active TSS	NH-A	brain
41	chr7:12249800-12251800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:12249800-12251800	Active TSS	Brain Cingulate Gyrus	brain
43	chr7:12249800-12251800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:12249800-12252000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:12249800-12252200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:12249800-12252200	Active TSS	Right Atrium	heart
47	chr7:12249800-12253000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr7:12250000-12250200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:12250000-12250200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr7:12250000-12250200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell

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