Variant report

Variant	rs3799290
Chromosome Location	chr6:74354952-74354953
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	chr6:74354599-74355022	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
2	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
3	chr6:74229165..74233433-chr6:74353361..74356645,5	MCF-7	breast:
4	chr6:74353596..74359738-chr6:74361541..74364786,8	MCF-7	breast:
5	chr6:74354143..74358709-chr6:74361254..74364709,5	MCF-7	breast:

Variant related genes	Relation type
SLC17A5	TF binding region
ENSG00000119899	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000229862	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10455093	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10455094	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10455095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10455279	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10455280	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943107	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10943108	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10943109	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10943111	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943114	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10943115	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750970	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11751984	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11758258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969324	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12154139	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12189643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190442	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190753	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191213	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12192476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199348	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199822	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12199937	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12201702	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201746	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202024	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12206001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207204	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12207961	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210690	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12212738	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12214293	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214539	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17758926	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734517	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757112	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799295	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3928609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706545	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4706546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708068	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698483	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56004619	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56390246	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438423	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62438424	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62438426	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62438431	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62440461	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440465	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440490	0.92[AMR][1000 genomes]
rs72947490	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9341427	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9352013	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	172 gene(s)	inside rSNPs	diseases
8	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74296400-74355000	Weak transcription	Fetal Brain Male	brain
2	chr6:74297000-74361800	Weak transcription	GM12878-XiMat	blood
3	chr6:74303400-74355000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:74307200-74362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:74307600-74356400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:74311200-74355000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:74314200-74362800	Weak transcription	Stomach Mucosa	stomach
8	chr6:74315600-74362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:74316600-74355000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:74318400-74355000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:74318800-74355200	Weak transcription	Colonic Mucosa	Colon
12	chr6:74324600-74362800	Weak transcription	Pancreas	Pancrea
13	chr6:74324800-74361600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:74325000-74355200	Weak transcription	HSMM	muscle
15	chr6:74325200-74355000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:74325400-74362800	Weak transcription	Small Intestine	intestine
17	chr6:74339200-74362800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:74341000-74355000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:74341400-74355000	Weak transcription	Aorta	Aorta
20	chr6:74341400-74355000	Weak transcription	Ovary	ovary
21	chr6:74341400-74360400	Weak transcription	HepG2	liver
22	chr6:74341600-74362800	Weak transcription	Esophagus	oesophagus
23	chr6:74341600-74362800	Weak transcription	Gastric	stomach
24	chr6:74341800-74355000	Weak transcription	Brain Angular Gyrus	brain
25	chr6:74341800-74362600	Weak transcription	Brain Substantia Nigra	brain
26	chr6:74342000-74362800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:74342400-74362800	Weak transcription	Lung	lung
28	chr6:74342400-74362800	Weak transcription	Spleen	Spleen
29	chr6:74343200-74362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:74343600-74355000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:74343600-74355400	Weak transcription	Placenta	Placenta
32	chr6:74344200-74355000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:74345000-74355200	Weak transcription	Fetal Thymus	thymus
34	chr6:74346000-74362200	Weak transcription	Hela-S3	cervix
35	chr6:74346600-74355000	Weak transcription	Psoas Muscle	Psoas
36	chr6:74346800-74355000	Weak transcription	Thymus	Thymus
37	chr6:74347000-74355000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr6:74347200-74355000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:74347200-74362800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:74348200-74355200	Weak transcription	Left Ventricle	heart
41	chr6:74348400-74355000	Weak transcription	NH-A	brain
42	chr6:74348400-74358200	Weak transcription	HSMMtube	muscle
43	chr6:74348600-74355000	Weak transcription	Brain Anterior Caudate	brain
44	chr6:74349000-74361600	Weak transcription	Dnd41	blood
45	chr6:74349400-74355000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:74349400-74355000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:74349400-74355400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:74349600-74362800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:74349800-74356800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:74350400-74355000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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