Variant report

Variant	rs56393713
Chromosome Location	chr6:29597182-29597183
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	chr6:29596057-29597183	K562	blood:	n/a	n/a
2	MXI1	chr6:29595456-29597598	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:29593077-29597878	K562	blood:	n/a	n/a
4	REST	chr6:29594215-29597204	H1-neurons	neurons:	n/a	chr6:29596563-29596573
5	MAZ	chr6:29594519-29597214	IMR90	lung:	n/a	chr6:29595569-29595578 chr6:29594847-29594856 chr6:29595685-29595695

No.	Distal block	Cell Line	Cell type
1	chr6:29597090..29598941-chr6:30025217..30026901,2	K562	blood:
2	chr6:28889101..28891643-chr6:29595051..29597893,2	K562	blood:
3	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
4	chr6:29596747..29597490-chr9:18419651..18420547,2	MCF-7	breast:
5	chr6:29572757..29580903-chr6:29593317..29599166,10	K562	blood:
6	chr6:29595494..29598412-chr6:29717928..29720060,2	K562	blood:

Variant related genes	Relation type
GABBR1	TF binding region
ENSG00000066379	Chromatin interaction
ENSG00000235821	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000199290	Chromatin interaction
ENSG00000272236	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs16895101	0.94[ASN][1000 genomes]
rs16895218	0.82[AMR][1000 genomes]
rs2057010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058325	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058326	0.83[ASN][1000 genomes]
rs28359971	0.85[ASN][1000 genomes]
rs28359972	0.87[ASN][1000 genomes]
rs28749524	0.87[ASN][1000 genomes]
rs29219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29233	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs29254	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs29256	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs29266	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3025628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362515	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs362517	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55701059	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55871431	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55888673	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55971964	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56020557	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56045105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56106029	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56142919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56155438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62392941	0.96[ASN][1000 genomes]
rs62392942	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392943	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392944	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62392946	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62406580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62406582	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62406583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406584	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72831507	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29593600-29598200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:29594600-29597200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:29594600-29597400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr6:29594800-29597200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:29594800-29597200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:29594800-29597200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr6:29594800-29597400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:29594800-29597600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:29594800-29598000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr6:29595000-29597200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:29595000-29598400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:29595200-29597200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:29595600-29597200	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr6:29595600-29598000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:29596000-29597200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:29596000-29597200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:29596000-29597200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:29596000-29597200	Flanking Active TSS	HMEC	breast
19	chr6:29596000-29597600	Flanking Active TSS	Dnd41	blood
20	chr6:29596200-29597200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
21	chr6:29596200-29597200	Flanking Active TSS	Osteobl	bone
22	chr6:29596200-29597400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:29596200-29597400	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr6:29596200-29597400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr6:29596200-29598000	Flanking Active TSS	K562	blood
26	chr6:29596400-29597200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:29596400-29597200	Enhancers	Fetal Heart	heart
28	chr6:29596400-29597200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr6:29596400-29597400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:29596400-29597800	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr6:29596600-29597200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:29596600-29597200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr6:29596600-29597200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr6:29596600-29597200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:29596600-29597200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr6:29596600-29597200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:29596600-29597200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:29596600-29597200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:29596600-29597200	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr6:29596600-29597200	Bivalent Enhancer	Fetal Intestine Small	intestine
41	chr6:29596600-29597200	Bivalent Enhancer	Fetal Thymus	thymus
42	chr6:29596600-29597200	Enhancers	Lung	lung
43	chr6:29596600-29597200	Enhancers	Stomach Mucosa	stomach
44	chr6:29596600-29597200	Flanking Bivalent TSS/Enh	Thymus	Thymus
45	chr6:29596600-29598000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:29596600-29598000	Flanking Active TSS	Fetal Brain Female	brain
47	chr6:29596800-29597200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr6:29596800-29597200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr6:29596800-29597200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:29596800-29597200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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