Variant report

Variant	rs1550526
Chromosome Location	chr6:13295515-13295516
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13276714..13280149-chr6:13292500..13295672,4	K562	blood:
2	chr6:13290208..13292111-chr6:13295404..13298068,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFOD1-1	chr6:13295507-13295620	ENSG00000215022.3

Variant related genes	Relation type
ENSG00000112137	Chromatin interaction
ENSG00000272379	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11759028	0.93[ASN][1000 genomes]
rs1223393	0.81[CEU][hapmap]
rs12697949	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs182148	0.90[CEU][hapmap];0.90[MEX][hapmap]
rs2002961	0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs202028	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs202030	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]
rs202034	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs202038	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202040	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202042	0.83[CEU][hapmap]
rs202044	0.83[CEU][hapmap]
rs202045	0.81[CEU][hapmap]
rs202048	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202053	0.83[CEU][hapmap]
rs202064	0.81[CEU][hapmap]
rs202069	0.90[CEU][hapmap]
rs202070	0.83[CEU][hapmap]
rs202071	0.83[CEU][hapmap]
rs202072	0.83[CEU][hapmap]
rs202073	0.83[CEU][hapmap]
rs35952102	0.96[ASN][1000 genomes]
rs377704	0.83[CEU][hapmap]
rs3800481	1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800483	0.96[ASN][1000 genomes]
rs3800484	0.96[ASN][1000 genomes]
rs3800485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3800486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3816209	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3823442	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3823443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3857594	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs405078	0.83[CEU][hapmap]
rs413120	0.83[CEU][hapmap]
rs441213	0.83[CEU][hapmap]
rs445714	0.83[CEU][hapmap]
rs453695	0.81[CEU][hapmap]
rs454563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475165	0.84[ASN][1000 genomes]
rs515111	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs543645	1.00[YRI][hapmap]
rs6909879	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs6914796	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6922200	0.84[ASN][1000 genomes]
rs6923757	0.84[ASN][1000 genomes]
rs6924855	0.84[ASN][1000 genomes]
rs7742398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7755309	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs8541	1.00[CEU][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878700	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs909508	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9296641	0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9296642	0.86[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9369976	0.84[ASN][1000 genomes]
rs9369978	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9369979	0.84[ASN][1000 genomes]
rs9473908	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs9473909	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9473929	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9473930	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[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:125 , 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	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
3	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
7	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
8	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:13288600-13296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
11	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
12	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
14	chr6:13289000-13295800	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:13290200-13302800	Weak transcription	NHEK	skin
18	chr6:13290400-13296200	Strong transcription	Fetal Thymus	thymus
19	chr6:13290400-13296800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr6:13290400-13310400	Strong transcription	Dnd41	blood
21	chr6:13290600-13295600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:13290600-13296800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
24	chr6:13290800-13296400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:13291000-13295800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:13291000-13297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:13291000-13297400	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
29	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine
30	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr6:13291400-13296400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:13291400-13297800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:13291400-13299600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:13291400-13300200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:13291400-13303600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:13291600-13295600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:13291600-13295600	Strong transcription	Brain Anterior Caudate	brain
38	chr6:13291600-13295600	Strong transcription	HSMMtube	muscle
39	chr6:13291600-13295800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:13291600-13295800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:13291600-13295800	Strong transcription	Adipose Nuclei	Adipose
42	chr6:13291600-13295800	Strong transcription	Brain Cingulate Gyrus	brain
43	chr6:13291600-13295800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:13291600-13296200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:13291600-13296200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:13291600-13296200	Strong transcription	Liver	Liver
47	chr6:13291600-13296200	Strong transcription	Brain Germinal Matrix	brain
48	chr6:13291600-13296400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:13291600-13296400	Strong transcription	Left Ventricle	heart
50	chr6:13291600-13297000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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