Variant report

Variant	rs9378309
Chromosome Location	chr6:1725885-1725886
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	chr6:1724262..1726680-chr6:1728353..1730358,2	K562	blood:
2	chr6:1610217..1612226-chr6:1723387..1726071,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054598	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1013064	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1986203	0.82[EUR][1000 genomes]
rs1986205	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2318106	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2318107	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4959150	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4959598	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4959600	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6596846	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6901836	0.95[EUR][1000 genomes]
rs6924173	0.85[EUR][1000 genomes]
rs6928775	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6928953	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6937688	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6940556	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6942353	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs764518	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7754428	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7754564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7754761	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9328068	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9378308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9378652	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9391928	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9392325	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9392327	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9392328	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9405148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9405507	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1695400-1729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
4	chr6:1706800-1726800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:1713400-1726000	Weak transcription	Dnd41	blood
6	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:1716600-1728200	Weak transcription	Liver	Liver
8	chr6:1717000-1726200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:1717600-1731600	Weak transcription	Aorta	Aorta
10	chr6:1718800-1731400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:1721200-1731600	Weak transcription	Right Atrium	heart
12	chr6:1721200-1746200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:1721200-1748800	Weak transcription	Osteobl	bone
14	chr6:1721400-1730600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:1721400-1739400	Weak transcription	Hela-S3	cervix
16	chr6:1721600-1726600	Weak transcription	Brain Substantia Nigra	brain
17	chr6:1721800-1728600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:1722000-1729400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:1722200-1727800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:1723000-1727600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:1723000-1743200	Strong transcription	HepG2	liver
22	chr6:1723800-1726800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:1724000-1726800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:1724000-1728000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:1724200-1727000	Strong transcription	Primary T cells from cord blood	blood
26	chr6:1724400-1726800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr6:1724800-1726200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr6:1724800-1727200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:1724800-1729800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:1725000-1727400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:1725000-1729200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr6:1725000-1729200	Weak transcription	Adipose Nuclei	Adipose
33	chr6:1725000-1729400	Weak transcription	Spleen	Spleen
34	chr6:1725000-1730600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:1725000-1737800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:1725200-1726200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr6:1725200-1726200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:1725200-1726200	Weak transcription	Gastric	stomach
39	chr6:1725200-1726200	Weak transcription	Pancreas	Pancrea
40	chr6:1725200-1726200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:1725200-1726600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:1725200-1727000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:1725200-1727600	Weak transcription	Ovary	ovary
44	chr6:1725200-1728600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr6:1725200-1729000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:1725200-1729200	Weak transcription	Esophagus	oesophagus
47	chr6:1725200-1729400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:1725200-1729600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:1725200-1730800	Weak transcription	GM12878-XiMat	blood
50	chr6:1725200-1733400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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