Variant report

Variant	rs4709489
Chromosome Location	chr6:161489488-161489489
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	POLR2A	chr6:161489414-161489956	H1-neurons	neurons:	n/a	n/a
2	EP300	chr6:161489195-161489770	SK-N-SH_RA	brain:	n/a	n/a
3	GATA3	chr6:161489154-161489813	SK-N-SH	brain:	n/a	chr6:161489503-161489510 chr6:161489501-161489511 chr6:161489492-161489509 chr6:161489502-161489510 chr6:161489501-161489510
4	KAP1	chr6:161488708-161489971	U2OS	brain:	n/a	n/a
5	EP300	chr6:161489163-161489705	SK-N-SH_RA	brain:	n/a	n/a
6	GATA3	chr6:161489180-161489746	SK-N-SH	brain:	n/a	chr6:161489503-161489510 chr6:161489501-161489511 chr6:161489492-161489509 chr6:161489502-161489510 chr6:161489501-161489510
7	GATA3	chr6:161489147-161489934	SH-SY5Y	brain:	n/a	chr6:161489503-161489510 chr6:161489501-161489511 chr6:161489492-161489509 chr6:161489502-161489510 chr6:161489501-161489510
8	GATA2	chr6:161489149-161490059	SH-SY5Y	brain:	n/a	chr6:161489503-161489510 chr6:161489501-161489511 chr6:161489492-161489509 chr6:161489501-161489510
9	KAP1	chr6:161488758-161490049	HEK293	kidney:	n/a	n/a
10	GATA3	chr6:161489205-161489827	MCF-7	breast:	n/a	chr6:161489503-161489510 chr6:161489501-161489511 chr6:161489492-161489509 chr6:161489502-161489510 chr6:161489501-161489510
11	EP300	chr6:161488773-161490198	SK-N-SH	brain:	n/a	n/a
12	TCF7L2	chr6:161488754-161489790	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:161485567..161487564-chr6:161487928..161489693,2	K562	blood:
2	chr6:161411361..161413960-chr6:161487882..161490552,2	MCF-7	breast:

Variant related genes	Relation type
MAP3K4	TF binding region
ENSG00000272841	Chromatin interaction
ENSG00000085511	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1001809	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194157	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464779	1.00[ASN][1000 genomes]
rs1464780	1.00[ASN][1000 genomes]
rs1543261	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562026	1.00[ASN][1000 genomes]
rs1982291	1.00[ASN][1000 genomes]
rs2872613	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4472323	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559074	1.00[ASN][1000 genomes]
rs4708898	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709486	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709490	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709491	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709492	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4709493	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709495	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709496	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs587501	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs615269	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs619393	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs628430	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs628923	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6455701	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645718	1.00[ASN][1000 genomes]
rs657551	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662541	0.89[AMR][1000 genomes]
rs668638	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs682110	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683549	1.00[ASN][1000 genomes]
rs6902332	1.00[ASN][1000 genomes]
rs6902760	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905942	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908283	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6913706	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918476	1.00[ASN][1000 genomes]
rs6919831	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925502	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925800	1.00[ASN][1000 genomes]
rs6929462	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933810	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705829	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705830	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738762	1.00[ASN][1000 genomes]
rs7753585	1.00[ASN][1000 genomes]
rs7760056	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9346846	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9355330	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355332	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355867	1.00[ASN][1000 genomes]
rs9355872	1.00[ASN][1000 genomes]
rs9355873	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9364585	1.00[ASN][1000 genomes]
rs9364586	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9365248	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9458126	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][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	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats 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	6 gene(s)	inside rSNPs	diseases
2	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161435000-161490400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:161449000-161494400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:161453600-161506600	Weak transcription	Small Intestine	intestine
4	chr6:161455200-161495800	Weak transcription	Fetal Brain Male	brain
5	chr6:161456400-161501600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:161459400-161508800	Weak transcription	Hela-S3	cervix
7	chr6:161459800-161496600	Weak transcription	Fetal Kidney	kidney
8	chr6:161459800-161502800	Weak transcription	HUVEC	blood vessel
9	chr6:161460000-161499200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:161460600-161495600	Weak transcription	HSMMtube	muscle
11	chr6:161462800-161497200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:161462800-161497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:161462800-161508200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:161463000-161491600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:161463400-161491600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:161463600-161495600	Weak transcription	Pancreas	Pancrea
17	chr6:161463800-161499200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:161470400-161495000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:161470600-161492000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:161470600-161493800	Weak transcription	Fetal Thymus	thymus
21	chr6:161470600-161508000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:161470800-161491600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:161470800-161491600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:161471000-161490400	Weak transcription	Lung	lung
25	chr6:161471000-161491600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:161471000-161503800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:161471200-161491600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr6:161471200-161492200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:161471200-161494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:161471400-161491800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:161471400-161500600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:161471600-161491600	Weak transcription	Fetal Lung	lung
33	chr6:161471600-161494400	Weak transcription	Osteobl	bone
34	chr6:161471800-161491600	Weak transcription	Liver	Liver
35	chr6:161472000-161491600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:161472000-161491600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:161472000-161492200	Weak transcription	Fetal Intestine Large	intestine
38	chr6:161472200-161491600	Weak transcription	HSMM	muscle
39	chr6:161472600-161492600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:161472800-161491600	Weak transcription	Placenta	Placenta
41	chr6:161473000-161491600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:161473000-161495000	Weak transcription	Adipose Nuclei	Adipose
43	chr6:161473000-161495600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:161473200-161490400	Weak transcription	Fetal Stomach	stomach
45	chr6:161473200-161496200	Weak transcription	Psoas Muscle	Psoas
46	chr6:161473800-161494200	Weak transcription	HepG2	liver
47	chr6:161474400-161490400	Weak transcription	Fetal Intestine Small	intestine
48	chr6:161474400-161490600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr6:161474800-161491600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr6:161477400-161492600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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