Variant report

Variant	rs6928601
Chromosome Location	chr6:56340803-56340804
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	GATA3	chr6:56340709-56341382	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr6:56340791-56341484	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr6:56340709-56341405	SK-N-SH	brain:	n/a	n/a
4	GATA2	chr6:56340661-56341397	SH-SY5Y	brain:	n/a	n/a
5	GATA3	chr6:56340661-56341368	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr6:56340484-56341269	SK-N-SH	brain:	n/a	n/a
7	EP300	chr6:56340098-56341541	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr6:56340727-56341421	SK-N-SH	brain:	n/a	n/a
9	RCOR1	chr6:56340696-56341175	Hela-S3	cervix:	n/a	n/a
10	EP300	chr6:56340785-56341162	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56335330..56337721-chr6:56339949..56341801,2	K562	blood:

Variant related genes	Relation type
DST	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11753813	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758339	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11759493	0.89[ASN][1000 genomes]
rs11961668	0.88[ASN][1000 genomes]
rs12174955	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204556	0.89[ASN][1000 genomes]
rs1359068	0.87[ASN][1000 genomes]
rs1359070	0.87[ASN][1000 genomes]
rs1535610	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1535612	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1570492	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273972	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273973	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273974	0.87[ASN][1000 genomes]
rs2397226	0.89[ASN][1000 genomes]
rs2894837	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34954984	0.89[ASN][1000 genomes]
rs35671304	0.87[ASN][1000 genomes]
rs35926142	0.89[ASN][1000 genomes]
rs4283892	0.89[ASN][1000 genomes]
rs4331988	0.84[ASN][1000 genomes]
rs4544910	0.87[ASN][1000 genomes]
rs45486696	0.89[ASN][1000 genomes]
rs4715625	0.87[ASN][1000 genomes]
rs59101638	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6459161	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459163	0.87[ASN][1000 genomes]
rs6904202	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6913572	0.87[ASN][1000 genomes]
rs6914325	0.82[EUR][1000 genomes]
rs6927258	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721475	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72877350	0.89[ASN][1000 genomes]
rs7746753	0.87[ASN][1000 genomes]
rs7755220	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296848	0.89[ASN][1000 genomes]
rs9349822	0.80[EUR][1000 genomes]
rs9349823	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349824	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349825	0.91[ASN][1000 genomes]
rs9370531	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9370534	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9370535	0.89[ASN][1000 genomes]
rs9382631	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382635	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9396211	0.82[EUR][1000 genomes]
rs9396213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396214	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9396215	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9396218	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9475709	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	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	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56315000-56347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:56315000-56349800	Strong transcription	HSMM	muscle
4	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:56317200-56342800	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr6:56319000-56348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:56319200-56348400	Strong transcription	NHDF-Ad	bronchial
8	chr6:56319400-56343600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:56319400-56344200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:56321000-56343400	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:56321200-56343800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:56322200-56349200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:56322400-56344200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:56322600-56348200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:56325000-56346600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:56327200-56351400	Weak transcription	Fetal Thymus	thymus
17	chr6:56328600-56362000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:56329200-56373800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr6:56330000-56351400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:56330000-56372400	Weak transcription	Lung	lung
21	chr6:56330200-56347200	Weak transcription	Small Intestine	intestine
22	chr6:56330200-56357400	Weak transcription	Esophagus	oesophagus
23	chr6:56332800-56342400	Strong transcription	HSMMtube	muscle
24	chr6:56332800-56346000	Strong transcription	Adipose Nuclei	Adipose
25	chr6:56332800-56349200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:56333000-56344400	Strong transcription	GM12878-XiMat	blood
27	chr6:56333000-56350000	Strong transcription	HMEC	breast
28	chr6:56333200-56341000	Strong transcription	Osteobl	bone
29	chr6:56333200-56342200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr6:56333200-56342200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:56333200-56342200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr6:56333200-56342400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:56333200-56342600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:56333200-56342600	Strong transcription	Fetal Muscle Leg	muscle
35	chr6:56333200-56343000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:56333200-56343000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr6:56333400-56342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:56334400-56348200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr6:56334400-56359400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:56334600-56341800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:56334600-56342400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:56334800-56342600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:56335200-56341600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:56336200-56342200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:56336400-56341600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:56336600-56342400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:56336600-56347400	Weak transcription	K562	blood
48	chr6:56337600-56348000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:56337600-56350800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:56337600-56351400	Weak transcription	Aorta	Aorta

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