Variant report

Variant	rs17663557
Chromosome Location	chr6:49463970-49463971
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	chr6:49462218-49464476	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49460315..49462517-chr6:49463838..49466982,4	K562	blood:

Variant related genes	Relation type
GLYATL3	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10948505	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]
rs10948506	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]
rs10948507	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189789	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12191171	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198507	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202875	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204398	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204617	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206768	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208117	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208221	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214010	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214609	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17663627	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127756	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127759	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229385	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57912929	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6928563	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755833	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]
rs7756016	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]
rs7774623	0.87[EUR][1000 genomes];0.90[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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1019611	chr6:49431569-49470663	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1793167	chr6:49459978-49466686	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1799212	chr6:49459978-49466791	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49432200-49465000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:49432600-49472000	Weak transcription	NHEK	skin
3	chr6:49440400-49465200	Weak transcription	HUVEC	blood vessel
4	chr6:49441000-49464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:49448400-49464600	Weak transcription	Gastric	stomach
6	chr6:49449800-49465000	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:49450400-49464200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:49450600-49464000	Weak transcription	Spleen	Spleen
9	chr6:49451400-49467400	Weak transcription	Fetal Intestine Small	intestine
10	chr6:49451600-49464000	Weak transcription	Fetal Stomach	stomach
11	chr6:49454000-49465200	Weak transcription	Fetal Brain Male	brain
12	chr6:49456400-49465000	Weak transcription	HSMMtube	muscle
13	chr6:49457000-49464800	Weak transcription	Fetal Kidney	kidney
14	chr6:49457200-49465000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:49458000-49464200	Weak transcription	Brain Germinal Matrix	brain
16	chr6:49458000-49466600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:49458400-49472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:49458600-49464000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:49458600-49464600	Weak transcription	Left Ventricle	heart
20	chr6:49458600-49473800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:49458800-49465000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:49459000-49464200	Weak transcription	Adipose Nuclei	Adipose
23	chr6:49459000-49464400	Weak transcription	Liver	Liver
24	chr6:49459000-49464400	Weak transcription	K562	blood
25	chr6:49460200-49465000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:49460400-49473200	Weak transcription	HepG2	liver
27	chr6:49460600-49464000	Weak transcription	Brain Anterior Caudate	brain
28	chr6:49460600-49464200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:49460600-49464600	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:49460600-49464800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:49460600-49473600	Weak transcription	Stomach Mucosa	stomach
32	chr6:49461000-49464200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:49461200-49465200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:49461400-49464200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:49461400-49472400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:49461600-49464600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr6:49461600-49466800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:49461800-49464200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:49461800-49467000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:49462200-49467000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:49462600-49464200	Weak transcription	Fetal Thymus	thymus
42	chr6:49462600-49464800	Weak transcription	Primary T cells from cord blood	blood
43	chr6:49462800-49464400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:49462800-49464600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:49462800-49465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:49463400-49465000	Weak transcription	Thymus	Thymus

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