Variant report

Variant	rs6561498
Chromosome Location	chr13:49704072-49704073
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49549163..49550802-chr13:49703003..49705467,2	K562	blood:

Variant related genes	Relation type
ENSG00000102531	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1407826	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1937182	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983806	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2987534	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012124	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012130	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012134	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942806	0.90[ASN][1000 genomes]
rs4942807	1.00[AMR][1000 genomes]
rs57277286	1.00[AMR][1000 genomes]
rs57590763	1.00[AMR][1000 genomes]
rs58064396	1.00[AMR][1000 genomes]
rs58372993	1.00[AMR][1000 genomes]
rs60882749	1.00[EUR][1000 genomes]
rs61192069	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61517389	1.00[AMR][1000 genomes]
rs6561495	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561508	1.00[AMR][1000 genomes]
rs6561516	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs6650333	1.00[AMR][1000 genomes]
rs7321706	0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs7326409	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7338704	1.00[CHB][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7999767	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs912193	0.85[ASN][1000 genomes]
rs912547	0.89[CHD][hapmap];0.89[JPT][hapmap]
rs928039	1.00[ASN][1000 genomes]
rs9316432	1.00[AMR][1000 genomes]
rs9535196	0.89[JPT][hapmap]

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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv1796840	chr13:49671215-49760666	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1052168	chr13:49691378-49743696	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49685600-49705400	Weak transcription	K562	blood
2	chr13:49687600-49705800	Weak transcription	Small Intestine	intestine
3	chr13:49687600-49706200	Weak transcription	Fetal Heart	heart
4	chr13:49687600-49724200	Weak transcription	Esophagus	oesophagus
5	chr13:49687600-49789000	Weak transcription	Stomach Mucosa	stomach
6	chr13:49688000-49705000	Weak transcription	Right Ventricle	heart
7	chr13:49689000-49711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr13:49690200-49705200	Weak transcription	Brain Anterior Caudate	brain
9	chr13:49691400-49705400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:49691800-49705200	Weak transcription	HMEC	breast
11	chr13:49692000-49705200	Weak transcription	NHLF	lung
12	chr13:49692800-49705200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:49693400-49705200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:49693400-49705200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr13:49693400-49705200	Weak transcription	Aorta	Aorta
16	chr13:49693400-49706600	Weak transcription	A549	lung
17	chr13:49693600-49704600	Weak transcription	Hela-S3	cervix
18	chr13:49693600-49705000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr13:49693600-49705000	Weak transcription	Fetal Intestine Small	intestine
20	chr13:49693600-49705000	Weak transcription	Fetal Stomach	stomach
21	chr13:49693600-49705000	Weak transcription	Gastric	stomach
22	chr13:49693600-49705200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr13:49693600-49705200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr13:49693600-49705200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr13:49693600-49705200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr13:49693600-49705200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr13:49693600-49705200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:49693600-49705200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr13:49693600-49705200	Weak transcription	Colonic Mucosa	Colon
30	chr13:49693600-49705200	Weak transcription	Lung	lung
31	chr13:49693600-49705200	Weak transcription	Ovary	ovary
32	chr13:49693600-49705200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:49693600-49705200	Weak transcription	Thymus	Thymus
34	chr13:49693600-49705200	Weak transcription	GM12878-XiMat	blood
35	chr13:49693600-49705400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:49693600-49705400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr13:49693600-49705400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:49693600-49705600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr13:49693600-49711000	Weak transcription	Pancreas	Pancrea
40	chr13:49693600-49737200	Weak transcription	Spleen	Spleen
41	chr13:49693800-49705200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr13:49693800-49705200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:49693800-49705200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr13:49693800-49705200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr13:49693800-49705200	Weak transcription	HSMM	muscle
46	chr13:49693800-49705200	Weak transcription	Osteobl	bone
47	chr13:49693800-49705400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr13:49694000-49705000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr13:49694000-49705200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr13:49694000-49705200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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