Variant report

Variant	rs942474
Chromosome Location	chr6:4029109-4029110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4028831..4031287-chr6:4036762..4038372,2	MCF-7	breast:
2	chr6:4017127..4021712-chr6:4024142..4029441,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272248	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000230648	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12174184	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1408457	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1543355	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1969837	0.81[EUR][1000 genomes]
rs2181894	0.94[ASN][1000 genomes]
rs2745451	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3747761	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747762	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747763	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3761787	0.97[ASN][1000 genomes]
rs4466281	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959916	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4959918	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4959919	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6900476	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905475	0.82[ASN][1000 genomes]
rs6906467	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910519	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914180	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6916982	0.94[ASN][1000 genomes]
rs6921738	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6930892	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933593	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6941706	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697745	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707980	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707981	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707982	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707983	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707984	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707985	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707987	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707988	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73349780	0.84[ASN][1000 genomes]
rs7744603	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7763233	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853396	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs853397	0.92[ASN][1000 genomes]
rs853398	0.93[ASN][1000 genomes]
rs853399	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853400	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853402	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs853403	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853404	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853405	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853406	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853407	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853408	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853410	0.83[ASN][1000 genomes]
rs853411	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs860477	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs860478	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9328215	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9328216	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9392546	0.83[EUR][1000 genomes]
rs9405217	0.83[EUR][1000 genomes]
rs9405694	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941443	0.94[ASN][1000 genomes]
rs9503893	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4022400-4043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:4022600-4049400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:4023000-4032000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:4023000-4038600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:4023200-4031800	Weak transcription	Placenta	Placenta
7	chr6:4023200-4034000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr6:4023200-4035600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:4023200-4043400	Weak transcription	Aorta	Aorta
10	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:4023400-4029200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:4023400-4038800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:4023400-4040600	Weak transcription	Fetal Brain Male	brain
14	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
15	chr6:4023600-4031000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:4023800-4030600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:4023800-4031200	Weak transcription	HUVEC	blood vessel
18	chr6:4023800-4032000	Weak transcription	Fetal Lung	lung
19	chr6:4023800-4032200	Weak transcription	Colonic Mucosa	Colon
20	chr6:4023800-4033600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:4023800-4037400	Weak transcription	Fetal Brain Female	brain
22	chr6:4023800-4037600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:4024000-4031400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:4024000-4031600	Weak transcription	NH-A	brain
26	chr6:4024000-4031800	Weak transcription	HMEC	breast
27	chr6:4024000-4035600	Weak transcription	NHLF	lung
28	chr6:4024000-4036400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:4024000-4037600	Weak transcription	HSMMtube	muscle
30	chr6:4024200-4031000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:4024200-4031400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:4024200-4037000	Weak transcription	Right Atrium	heart
33	chr6:4024200-4040200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:4024400-4029200	Genic enhancers	HepG2	liver
35	chr6:4024400-4031800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:4024400-4035800	Weak transcription	Thymus	Thymus
37	chr6:4024600-4031400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr6:4024600-4031400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:4024600-4031600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:4024600-4032000	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:4024600-4036600	Weak transcription	Spleen	Spleen
42	chr6:4024600-4040200	Weak transcription	Esophagus	oesophagus
43	chr6:4024600-4059200	Strong transcription	Fetal Thymus	thymus
44	chr6:4025000-4029800	Weak transcription	Pancreas	Pancrea
45	chr6:4025200-4031800	Weak transcription	Liver	Liver
46	chr6:4025200-4039200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:4025400-4037600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:4025800-4031600	Weak transcription	Brain Germinal Matrix	brain
49	chr6:4025800-4034000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:4026000-4032000	Weak transcription	Adipose Nuclei	Adipose

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