Variant report

Variant	rs4959600
Chromosome Location	chr6:1730666-1730667
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1729734..1732715-chr8:102478576..102480774,2	MCF-7	breast:
2	chr6:1728980..1730810-chr6:1735730..1738252,2	MCF-7	breast:
3	chr22:50964903..50965473-chr6:1730306..1731136,2	Hela-S3	cervix:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1013064	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1986203	0.82[EUR][1000 genomes]
rs1986204	0.81[EUR][1000 genomes]
rs1986205	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2318106	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2318107	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4129868	0.84[AFR][1000 genomes]
rs4959150	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4959598	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6596846	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6901836	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs6924173	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs6928775	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6928953	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6937688	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6940556	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs6942353	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs764518	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7754428	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7754564	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7754761	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9328068	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9378308	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9378309	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9378652	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9391928	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9392325	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9392327	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9392328	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9392330	1.00[CEU][hapmap]
rs9405148	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9405507	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
2	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
3	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:1717600-1731600	Weak transcription	Aorta	Aorta
5	chr6:1718800-1731400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:1721200-1731600	Weak transcription	Right Atrium	heart
7	chr6:1721200-1746200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:1721200-1748800	Weak transcription	Osteobl	bone
9	chr6:1721400-1739400	Weak transcription	Hela-S3	cervix
10	chr6:1723000-1743200	Strong transcription	HepG2	liver
11	chr6:1725000-1737800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:1725200-1730800	Weak transcription	GM12878-XiMat	blood
13	chr6:1725200-1733400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:1725400-1735600	Weak transcription	Stomach Mucosa	stomach
15	chr6:1726800-1730800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:1726800-1731600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:1726800-1735400	Weak transcription	Gastric	stomach
18	chr6:1726800-1735600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:1726800-1749000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:1726800-1749000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:1727000-1735600	Weak transcription	Pancreas	Pancrea
22	chr6:1727000-1737600	Weak transcription	Primary T cells from cord blood	blood
23	chr6:1728400-1730800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:1728600-1730800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:1728600-1731600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:1729000-1731000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:1729200-1730800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:1729400-1730800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr6:1730200-1730800	Enhancers	HMEC	breast
30	chr6:1730400-1730800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr6:1730400-1731000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:1730400-1731200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:1730400-1733000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:1730600-1730800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:1730600-1732200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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