Variant report

Variant	rs6596846
Chromosome Location	chr6:1719947-1719948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1719377..1721918-chr6:1724599..1726722,2	MCF-7	breast:
2	chr6:1709833..1714241-chr6:1719630..1722826,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112699	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1013064	0.89[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1986205	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2318106	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2318107	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4129868	1.00[AFR][1000 genomes]
rs4959150	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4959598	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4959600	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6901836	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs6924173	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6928775	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6928953	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6937688	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6940556	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6942353	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs761147	0.81[CEU][hapmap]
rs764518	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7754428	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7754564	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7754761	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9328068	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9378308	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9378309	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9378652	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9391928	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9392325	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9392327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9392328	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9392330	1.00[CEU][hapmap]
rs9405148	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9405507	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv432843	chr6:1694719-1725261	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6596846	GMDS,FLJ46552	cis	brain	BrainEAC

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1694200-1724400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:1695400-1729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
4	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
5	chr6:1703600-1720800	Weak transcription	Right Atrium	heart
6	chr6:1704000-1721000	Weak transcription	Lung	lung
7	chr6:1704200-1725200	Weak transcription	Primary B cells from cord blood	blood
8	chr6:1704600-1720800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:1705800-1724000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:1706000-1724200	Weak transcription	NHEK	skin
11	chr6:1706800-1726800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:1707200-1724600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:1707800-1724600	Weak transcription	GM12878-XiMat	blood
14	chr6:1708200-1724600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:1709800-1720800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:1709800-1724400	Weak transcription	Spleen	Spleen
17	chr6:1711000-1724200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:1712400-1720800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:1713400-1724800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:1713400-1726000	Weak transcription	Dnd41	blood
21	chr6:1713800-1722800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:1715800-1720800	Weak transcription	Left Ventricle	heart
23	chr6:1715800-1724400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:1716400-1724800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:1716600-1728200	Weak transcription	Liver	Liver
27	chr6:1716800-1720800	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:1717000-1726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:1717600-1723800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:1717600-1724200	Weak transcription	Primary T cells from cord blood	blood
31	chr6:1717600-1731600	Weak transcription	Aorta	Aorta
32	chr6:1717800-1721800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:1718800-1720600	Weak transcription	Fetal Kidney	kidney
34	chr6:1718800-1723800	Weak transcription	Placenta	Placenta
35	chr6:1718800-1724400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr6:1718800-1724600	Weak transcription	Gastric	stomach
37	chr6:1718800-1724800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:1718800-1724800	Weak transcription	Pancreas	Pancrea
39	chr6:1718800-1731400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:1719400-1720400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:1719600-1720800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:1719800-1720200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:1719800-1721800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:1719800-1723000	Weak transcription	HepG2	liver
45	chr6:1719800-1725800	Weak transcription	Fetal Intestine Small	intestine

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