Variant report

Variant	rs202030
Chromosome Location	chr6:13292152-13292153
allele	C/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	CTCF	chr6:13292059-13292176	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:13291626-13292188	K562	blood:	n/a	n/a
3	CTCF	chr6:13292035-13292152	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:13284835-13292200	GM12878	blood:	n/a	n/a
5	CTCF	chr6:13292040-13292190	GM12871	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13288763..13290813-chr6:13291778..13294382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272379	TF binding region
ENSG00000272379	Chromatin interaction

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

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

rs_ID	r²[population]
rs11759028	0.88[ASN][1000 genomes]
rs1223393	0.81[CEU][hapmap]
rs12697949	0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs1550526	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs182148	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2002961	0.84[JPT][hapmap]
rs202028	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202034	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202042	0.83[CEU][hapmap];0.80[ASN][1000 genomes]
rs202044	0.83[CEU][hapmap];0.81[ASN][1000 genomes]
rs202045	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs202046	0.81[ASN][1000 genomes]
rs202048	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs202053	0.83[CEU][hapmap]
rs202064	0.81[CEU][hapmap]
rs202068	0.81[EUR][1000 genomes]
rs202069	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs202070	0.83[CEU][hapmap]
rs202071	0.83[CEU][hapmap]
rs202072	0.83[CEU][hapmap]
rs202073	0.83[CEU][hapmap]
rs35952102	0.91[ASN][1000 genomes]
rs375661	0.80[ASN][1000 genomes]
rs377704	0.83[CEU][hapmap]
rs3800481	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3800482	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[ASN][1000 genomes]
rs3800483	0.91[ASN][1000 genomes]
rs3800484	0.91[ASN][1000 genomes]
rs3800485	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs3800486	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3823442	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3823443	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3857594	0.84[JPT][hapmap]
rs405078	0.83[CEU][hapmap];0.80[ASN][1000 genomes]
rs413120	0.83[CEU][hapmap]
rs441213	0.83[CEU][hapmap]
rs445714	0.83[CEU][hapmap];0.80[ASN][1000 genomes]
rs453695	0.81[CEU][hapmap]
rs454563	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4602719	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs495895	0.80[ASN][1000 genomes]
rs515111	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909879	0.84[JPT][hapmap]
rs6914796	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7742398	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7755309	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs8541	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878700	0.84[JPT][hapmap]
rs909508	0.84[JPT][hapmap]
rs9296641	0.84[JPT][hapmap]
rs9296642	0.84[JPT][hapmap]
rs9369978	0.84[JPT][hapmap]
rs9473908	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs9473909	0.84[JPT][hapmap]
rs9473929	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9473930	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:13280000-13292600	Weak transcription	NHLF	lung
4	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:13284000-13293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
8	chr6:13285800-13293000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:13285800-13293000	Weak transcription	Brain Substantia Nigra	brain
10	chr6:13286600-13292800	Weak transcription	Colonic Mucosa	Colon
11	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:13287200-13292800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:13287400-13294400	Weak transcription	Fetal Kidney	kidney
14	chr6:13287800-13294200	Weak transcription	A549	lung
15	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:13288000-13292200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:13288000-13294600	Weak transcription	Fetal Brain Male	brain
19	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr6:13288200-13292600	Weak transcription	Placenta	Placenta
21	chr6:13288200-13294200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:13288200-13294200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:13288200-13295400	Weak transcription	Fetal Heart	heart
24	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
25	chr6:13288400-13293200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:13288400-13294200	Weak transcription	Osteobl	bone
27	chr6:13288400-13294800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
29	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr6:13288600-13292400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:13288600-13293800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:13288600-13294200	Weak transcription	Esophagus	oesophagus
33	chr6:13288600-13295000	Strong transcription	Primary B cells from cord blood	blood
34	chr6:13288600-13295000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:13288600-13296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
37	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
38	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
40	chr6:13288800-13293000	Weak transcription	Fetal Lung	lung
41	chr6:13288800-13294200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:13289000-13292400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:13289000-13295800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:13289200-13294000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:13289200-13294200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:13289400-13292800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:13289400-13293000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:13289600-13292600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:13289600-13292800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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