Variant report

Variant	rs4959918
Chromosome Location	chr6:4038952-4038953
allele	C/T
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	chr6:4038739-4039045	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:4038621-4039949	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4038263..4039862-chr6:4134897..4137709,2	K562	blood:
2	chr6:4038415..4040524-chr6:4062857..4065779,3	K562	blood:

Variant related genes	Relation type
PRPF4B	TF binding region
ENSG00000198721	Chromatin interaction
ENSG00000234817	Chromatin interaction
ENSG00000254821	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12174184	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1408457	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1543355	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2181894	0.90[ASN][1000 genomes]
rs2745451	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2745452	0.85[EUR][1000 genomes]
rs3747761	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747762	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3747763	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3761787	0.97[ASN][1000 genomes]
rs4466281	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959916	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959919	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6900476	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6905475	0.82[ASN][1000 genomes]
rs6906467	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6910519	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6914180	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6916982	0.90[ASN][1000 genomes]
rs6921738	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6930892	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6933593	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6941706	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs697745	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707980	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707981	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707982	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707983	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707984	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707985	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs707987	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs707988	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73349780	0.84[ASN][1000 genomes]
rs7744603	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7763233	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853396	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs853397	0.92[ASN][1000 genomes]
rs853398	0.93[ASN][1000 genomes]
rs853399	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853400	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs853402	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs853403	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853404	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853405	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853406	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853407	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853408	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853409	0.82[ASN][1000 genomes]
rs853410	0.84[ASN][1000 genomes]
rs853411	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs860477	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs860478	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9328215	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9328216	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9405694	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941443	0.90[ASN][1000 genomes]
rs942474	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9503893	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1034223	chr6:4030708-4060347	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 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	chr6:4023000-4063600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:4023200-4043400	Weak transcription	Aorta	Aorta
5	chr6:4023200-4064000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:4023400-4040600	Weak transcription	Fetal Brain Male	brain
7	chr6:4023400-4071600	Weak transcription	Stomach Mucosa	stomach
8	chr6:4023800-4067000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:4024200-4040200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:4024600-4040200	Weak transcription	Esophagus	oesophagus
11	chr6:4024600-4059200	Strong transcription	Fetal Thymus	thymus
12	chr6:4025200-4039200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:4027200-4058200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:4027400-4039600	Weak transcription	Fetal Heart	heart
15	chr6:4027400-4039600	Weak transcription	Gastric	stomach
16	chr6:4027800-4040800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:4027800-4041600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:4028600-4039000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:4028800-4039600	Weak transcription	Brain Angular Gyrus	brain
20	chr6:4028800-4042000	Weak transcription	Right Ventricle	heart
21	chr6:4029000-4039200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:4029200-4040200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:4030000-4040600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:4030600-4039600	Weak transcription	Pancreas	Pancrea
25	chr6:4030600-4065800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:4030800-4059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:4030800-4066600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:4031000-4059200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:4031000-4066400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:4031200-4066600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr6:4031400-4040000	Weak transcription	Small Intestine	intestine
32	chr6:4033400-4039400	Weak transcription	HMEC	breast
33	chr6:4033400-4055200	Strong transcription	K562	blood
34	chr6:4033800-4054400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:4034000-4066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:4034400-4040200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:4034600-4040000	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:4035600-4040000	Strong transcription	NHLF	lung
39	chr6:4035600-4042400	Strong transcription	Fetal Intestine Small	intestine
40	chr6:4035600-4045800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:4035600-4063600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:4035600-4064200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr6:4035800-4042400	Strong transcription	Fetal Stomach	stomach
44	chr6:4035800-4046800	Strong transcription	Fetal Muscle Leg	muscle
45	chr6:4035800-4047200	Strong transcription	Fetal Intestine Large	intestine
46	chr6:4035800-4047200	Strong transcription	Thymus	Thymus
47	chr6:4035800-4051200	Strong transcription	Primary B cells from cord blood	blood
48	chr6:4035800-4052000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr6:4035800-4054400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:4035800-4057400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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