Variant report

Variant	rs3799288
Chromosome Location	chr6:74362900-74362901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74353596..74359738-chr6:74361541..74364786,8	MCF-7	breast:
2	chr6:74362119..74363006-chr6:74442455..74443360,3	MCF-7	breast:
3	chr6:74351063..74355074-chr6:74360720..74363620,5	K562	blood:
4	chr6:74228702..74232744-chr6:74360665..74366385,13	MCF-7	breast:
5	chr6:74229968..74230929-chr6:74362111..74362922,2	MCF-7	breast:
6	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
7	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
8	chr6:74103315..74106293-chr6:74362194..74365078,3	MCF-7	breast:
9	chr6:74228067..74234767-chr6:74357105..74365312,16	MCF-7	breast:
10	chr6:74354143..74358709-chr6:74361254..74364709,5	MCF-7	breast:
11	chr6:74234985..74236932-chr6:74360713..74363466,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000229862	Chromatin interaction
ENSG00000223967	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000119899	Chromatin interaction
ENSG00000203907	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10455281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10943112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943117	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964414	0.86[ASN][1000 genomes]
rs12189556	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195068	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195584	0.86[ASN][1000 genomes]
rs12196281	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197318	0.86[ASN][1000 genomes]
rs12197927	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12203363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210825	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211279	1.00[ASN][1000 genomes]
rs12212297	0.86[ASN][1000 genomes]
rs12213067	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213868	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216092	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13193629	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13207999	1.00[ASN][1000 genomes]
rs13211453	1.00[ASN][1000 genomes]
rs13212809	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351118	1.00[ASN][1000 genomes]
rs2351119	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2351120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2351121	1.00[ASN][1000 genomes]
rs34342150	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34613232	1.00[ASN][1000 genomes]
rs35256309	0.86[ASN][1000 genomes]
rs35468063	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35584640	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35659919	0.86[ASN][1000 genomes]
rs35733187	1.00[ASN][1000 genomes]
rs36131846	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3757109	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708065	1.00[ASN][1000 genomes]
rs56086551	0.84[EUR][1000 genomes]
rs59383274	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438456	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440462	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72949387	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744053	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784805	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	esv3408073	chr6:74362256-74364804	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr6:74361800-74363000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:74361800-74363200	Flanking Active TSS	Dnd41	blood
3	chr6:74361800-74364200	Active TSS	NH-A	brain
4	chr6:74361800-74364400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:74361800-74364600	Active TSS	Fetal Intestine Large	intestine
6	chr6:74361800-74364800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:74361800-74364800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:74361800-74364800	Active TSS	K562	blood
9	chr6:74361800-74365200	Active TSS	NHDF-Ad	bronchial
10	chr6:74362000-74363000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:74362000-74364400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:74362000-74364400	Active TSS	Brain Anterior Caudate	brain
13	chr6:74362000-74364400	Active TSS	Fetal Muscle Leg	muscle
14	chr6:74362000-74364600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:74362000-74364600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:74362000-74364600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:74362200-74363000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr6:74362200-74363000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:74362200-74363000	Flanking Active TSS	HUVEC	blood vessel
20	chr6:74362200-74364400	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:74362200-74364400	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:74362200-74364400	Active TSS	Fetal Intestine Small	intestine
23	chr6:74362200-74364400	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr6:74362200-74364400	Active TSS	GM12878-XiMat	blood
25	chr6:74362200-74364400	Active TSS	Hela-S3	cervix
26	chr6:74362200-74364400	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:74362200-74364600	Active TSS	NHLF	lung
28	chr6:74362200-74364800	Active TSS	Duodenum Mucosa	Duodenum
29	chr6:74362200-74365000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:74362200-74365000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr6:74362200-74365000	Active TSS	HSMMtube	muscle
32	chr6:74362400-74363000	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr6:74362400-74363000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr6:74362400-74363200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr6:74362400-74363400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:74362400-74364000	Active TSS	Primary T cells fromperipheralblood	blood
37	chr6:74362400-74364000	Active TSS	Fetal Thymus	thymus
38	chr6:74362400-74364200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr6:74362400-74364200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:74362400-74364200	Active TSS	Fetal Muscle Trunk	muscle
41	chr6:74362400-74364400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:74362400-74364400	Active TSS	Muscle Satellite Cultured Cells	--
43	chr6:74362400-74364400	Active TSS	Brain Angular Gyrus	brain
44	chr6:74362400-74364400	Active TSS	Brain Cingulate Gyrus	brain
45	chr6:74362400-74364400	Active TSS	Fetal Kidney	kidney
46	chr6:74362400-74364400	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr6:74362400-74364400	Active TSS	Thymus	Thymus
48	chr6:74362400-74364400	Active TSS	HMEC	breast
49	chr6:74362400-74364600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr6:74362400-74364600	Active TSS	H1 Cell Line	embryonic stem cell

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