Variant report

Variant	rs4959916
Chromosome Location	chr6:4025763-4025764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:4025736-4026107	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:4025235-4026255	K562	blood:	n/a	n/a
3	STAT3	chr6:4025739-4026037	MCF10A-Er-Src	breast:	n/a	chr6:4025904-4025912 chr6:4025901-4025915 chr6:4025902-4025913

No.	Distal block	Cell Line	Cell type
1	chr6:4025697..4028241-chr6:4039575..4042177,3	MCF-7	breast:
2	chr6:4017127..4021712-chr6:4024142..4029441,9	MCF-7	breast:
3	chr6:4025744..4028547-chr6:4034826..4037755,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230648	TF binding region
ENSG00000230648	Chromatin interaction
ENSG00000272248	Chromatin interaction
ENSG00000112739	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12174184	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408457	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543355	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1969837	0.83[EUR][1000 genomes]
rs2181894	0.95[ASN][1000 genomes]
rs2745451	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2745452	0.81[EUR][1000 genomes]
rs3747761	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747762	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747763	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761787	0.98[ASN][1000 genomes]
rs4466281	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959918	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959919	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6900476	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905475	0.83[ASN][1000 genomes]
rs6906467	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910519	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914180	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916982	0.95[ASN][1000 genomes]
rs6921738	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930892	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933593	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6941706	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs697745	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707980	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707981	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707982	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707983	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707984	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707985	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs707987	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs707988	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73349780	0.84[ASN][1000 genomes]
rs7744603	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7763233	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853396	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs853397	0.93[ASN][1000 genomes]
rs853398	0.94[ASN][1000 genomes]
rs853399	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853400	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853402	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs853403	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853404	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853405	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853406	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853407	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853408	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853409	0.81[ASN][1000 genomes]
rs853410	0.83[ASN][1000 genomes]
rs853411	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs860477	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860478	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9328215	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328216	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9392546	0.81[EUR][1000 genomes]
rs9405217	0.81[EUR][1000 genomes]
rs9405694	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941443	0.95[ASN][1000 genomes]
rs942474	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503893	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	chr6:4022400-4028400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:4022400-4043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:4022600-4049400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:4023000-4025800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:4023000-4027000	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr6:4023000-4027000	Weak transcription	Left Ventricle	heart
7	chr6:4023000-4028400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:4023000-4028400	Weak transcription	Ovary	ovary
9	chr6:4023000-4032000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:4023000-4038600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:4023200-4025800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:4023200-4027600	Weak transcription	Brain Angular Gyrus	brain
14	chr6:4023200-4028400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:4023200-4031800	Weak transcription	Placenta	Placenta
16	chr6:4023200-4034000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr6:4023200-4035600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:4023200-4043400	Weak transcription	Aorta	Aorta
19	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:4023400-4026000	Enhancers	Adipose Nuclei	Adipose
21	chr6:4023400-4026400	Enhancers	Colon Smooth Muscle	Colon
22	chr6:4023400-4027000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:4023400-4027600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:4023400-4029200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:4023400-4038800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:4023400-4040600	Weak transcription	Fetal Brain Male	brain
27	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
28	chr6:4023600-4026000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:4023600-4027400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:4023600-4028400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr6:4023600-4031000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:4023800-4025800	Weak transcription	A549	lung
33	chr6:4023800-4026200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:4023800-4027000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:4023800-4027000	Weak transcription	NHEK	skin
36	chr6:4023800-4027000	Weak transcription	Osteobl	bone
37	chr6:4023800-4027600	Weak transcription	Brain Substantia Nigra	brain
38	chr6:4023800-4027600	Weak transcription	HSMM	muscle
39	chr6:4023800-4030600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:4023800-4031200	Weak transcription	HUVEC	blood vessel
41	chr6:4023800-4032000	Weak transcription	Fetal Lung	lung
42	chr6:4023800-4032200	Weak transcription	Colonic Mucosa	Colon
43	chr6:4023800-4033600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr6:4023800-4037400	Weak transcription	Fetal Brain Female	brain
45	chr6:4023800-4037600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:4024000-4025800	Enhancers	Right Ventricle	heart
48	chr6:4024000-4026200	Enhancers	Primary T cells from cord blood	blood
49	chr6:4024000-4027000	Weak transcription	Primary B cells from cord blood	blood
50	chr6:4024000-4028400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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