Variant report

Variant	rs3800023
Chromosome Location	chr6:56965696-56965697
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:56965646-56965990	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:56963098-56971077	K562	blood:	n/a	n/a
3	POLR2A	chr6:56965552-56965850	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:56963370..56965802-chr6:56977570..56979666,2	K562	blood:
2	chr6:56911352..56913396-chr6:56964488..56966210,2	K562	blood:
3	chr6:56733407..56736067-chr6:56965444..56967288,2	K562	blood:
4	chr6:56918758..56920870-chr6:56963743..56966191,2	K562	blood:
5	chr6:56963536..56966458-chr6:57038304..57040042,2	K562	blood:
6	chr6:56954866..56956566-chr6:56964924..56967496,2	MCF-7	breast:
7	chr6:56818562..56821573-chr6:56964600..56969072,4	K562	blood:

No data

Variant related genes	Relation type
ZNF451	TF binding region
ENSG00000216854	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000168116	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000151914	Chromatin interaction
ENSG00000112200	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1020550	0.90[ASN][1000 genomes]
rs1044670	0.88[CEU][hapmap]
rs10456192	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10484410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11398	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12190575	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192222	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194288	0.90[ASN][1000 genomes]
rs12194407	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198801	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201039	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211901	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12214119	0.94[EUR][1000 genomes]
rs12214882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1547226	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16888392	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17619360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3800025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3957366	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs3996934	0.90[ASN][1000 genomes]
rs3996935	0.90[ASN][1000 genomes]
rs3996936	0.90[ASN][1000 genomes]
rs4523090	0.90[ASN][1000 genomes]
rs4631287	0.90[ASN][1000 genomes]
rs6459178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6918222	0.85[EUR][1000 genomes]
rs6936506	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72868608	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73463742	0.80[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7753547	0.90[ASN][1000 genomes]
rs7756421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7771115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349841	0.85[ASN][1000 genomes]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9396256	0.90[ASN][1000 genomes]
rs986245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3800023	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs3800023	BEND6	cis	Muscle Skeletal	GTEx
rs3800023	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56954000-56966800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:56955200-56965800	Weak transcription	Esophagus	oesophagus
3	chr6:56957000-56965800	Weak transcription	Stomach Mucosa	stomach
4	chr6:56957600-56967600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:56958200-56979600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:56958800-56974000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:56959200-56968200	Strong transcription	Fetal Intestine Large	intestine
8	chr6:56959200-56975000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:56959600-56968600	Strong transcription	Primary B cells from peripheral blood	blood
10	chr6:56959600-56969400	Strong transcription	Fetal Thymus	thymus
11	chr6:56959800-56969600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:56960200-56969600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr6:56961600-56969200	Strong transcription	Fetal Muscle Leg	muscle
14	chr6:56961600-56971000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:56961800-56968200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:56961800-56969000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:56961800-56969000	Strong transcription	GM12878-XiMat	blood
18	chr6:56961800-56969200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr6:56961800-56969600	Strong transcription	HUVEC	blood vessel
20	chr6:56961800-56970200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:56961800-56971000	Strong transcription	Placenta	Placenta
22	chr6:56961800-56972200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:56961800-56972200	Strong transcription	Dnd41	blood
24	chr6:56961800-56973400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:56961800-56975400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:56962000-56967800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr6:56962000-56968400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:56962000-56968400	Strong transcription	Hela-S3	cervix
29	chr6:56962000-56968600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr6:56962000-56968600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:56962000-56969400	Strong transcription	Primary B cells from cord blood	blood
32	chr6:56962000-56969600	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr6:56962000-56969800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr6:56962000-56969800	Strong transcription	Fetal Brain Female	brain
35	chr6:56962000-56970400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:56962000-56971000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:56962200-56968400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:56962200-56971000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:56962400-56967800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:56962400-56968000	Strong transcription	K562	blood
41	chr6:56962400-56968200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:56962600-56968000	Strong transcription	HSMM	muscle
43	chr6:56962600-56969600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:56962600-56969800	Strong transcription	NH-A	brain
45	chr6:56962600-56969800	Strong transcription	Osteobl	bone
46	chr6:56962600-56971000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:56962600-56971600	Strong transcription	NHEK	skin
48	chr6:56962600-56974400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:56962800-56968400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr6:56963000-56968000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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