Variant report

Variant	rs6899746
Chromosome Location	chr6:38412788-38412789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38411269..38413093-chr6:38413488..38416191,2	K562	blood:
2	chr6:38410346..38413041-chr6:38421338..38423278,2	MCF-7	breast:
3	chr6:38409873..38411784-chr6:38412186..38413893,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12191714	1.00[JPT][hapmap]
rs12206324	1.00[JPT][hapmap]
rs12206905	1.00[JPT][hapmap]
rs12212983	1.00[JPT][hapmap]
rs12215850	1.00[JPT][hapmap]
rs1883610	0.86[JPT][hapmap]
rs1983605	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs28445226	1.00[JPT][hapmap]
rs4236058	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4711542	1.00[JPT][hapmap]
rs4711546	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714152	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714157	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4714161	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714164	0.85[ASN][1000 genomes]
rs4714165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60936387	0.86[ASN][1000 genomes]
rs61192259	0.86[ASN][1000 genomes]
rs6458054	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909898	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6933268	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs6933758	0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6940319	1.00[JPT][hapmap]
rs742515	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7748599	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7749685	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7759629	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7766214	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7770868	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs871183	1.00[JPT][hapmap]
rs9349073	1.00[JPT][hapmap]
rs9357272	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9380743	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9394495	1.00[JPT][hapmap]
rs9394500	0.85[ASN][1000 genomes]
rs9470885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470888	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs9470891	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
2	chr6:38398800-38413800	Weak transcription	Aorta	Aorta
3	chr6:38404800-38413800	Weak transcription	Small Intestine	intestine
4	chr6:38405200-38413800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:38405200-38420800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:38405400-38413000	Weak transcription	Fetal Heart	heart
7	chr6:38408200-38419200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:38409200-38413800	Weak transcription	Ovary	ovary
9	chr6:38411600-38412800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:38411600-38412800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:38412000-38413000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:38412000-38413200	Weak transcription	Brain Substantia Nigra	brain
13	chr6:38412000-38413800	Weak transcription	Right Atrium	heart
14	chr6:38412000-38414000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:38412000-38415800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:38412000-38415800	Weak transcription	Psoas Muscle	Psoas
17	chr6:38412200-38413000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:38412200-38413800	Weak transcription	Brain Anterior Caudate	brain
19	chr6:38412200-38414000	Weak transcription	Spleen	Spleen
20	chr6:38412200-38445600	Weak transcription	Primary T cells from cord blood	blood
21	chr6:38412600-38419000	Weak transcription	Primary hematopoietic stem cells	blood

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