Variant report

Variant	rs62421869
Chromosome Location	chr6:71222921-71222922
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf57-4	chr6:71221818-71225656	NONHSAT113450

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13194594	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13197182	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13198944	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13207234	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13210191	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13218183	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13220004	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17634619	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28360504	0.84[EUR][1000 genomes]
rs34238069	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34257638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34401692	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34710086	0.84[EUR][1000 genomes]
rs34798144	0.83[EUR][1000 genomes]
rs35371002	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35426375	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35457911	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35462174	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35542509	0.87[EUR][1000 genomes]
rs57836066	0.85[EUR][1000 genomes]
rs62419669	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62420323	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62420326	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62421394	0.87[EUR][1000 genomes]
rs62421868	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62421874	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421877	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs997350	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
6	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv886146	chr6:71219464-71317480	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71210600-71262000	Weak transcription	Fetal Thymus	thymus
2	chr6:71214000-71236600	Weak transcription	Primary B cells from cord blood	blood
3	chr6:71214000-71244800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:71214000-71248600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:71214000-71248800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:71214000-71249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:71214000-71250600	Weak transcription	Right Ventricle	heart
8	chr6:71214000-71253000	Weak transcription	Colonic Mucosa	Colon
9	chr6:71214000-71253000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:71214000-71256600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:71214000-71276000	Weak transcription	Brain Angular Gyrus	brain
12	chr6:71214000-71276000	Weak transcription	Brain Germinal Matrix	brain
13	chr6:71214000-71276000	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:71214200-71225800	Weak transcription	Ovary	ovary
15	chr6:71214200-71234000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:71214200-71234400	Weak transcription	Liver	Liver
17	chr6:71214200-71248200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:71214400-71224800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:71214400-71226200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:71214400-71226200	Weak transcription	Fetal Brain Male	brain
21	chr6:71214400-71234200	Weak transcription	HepG2	liver
22	chr6:71214400-71238200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:71214400-71246000	Weak transcription	HMEC	breast
24	chr6:71214400-71251000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:71214400-71251800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr6:71214400-71257000	Weak transcription	Brain Anterior Caudate	brain
27	chr6:71214400-71262000	Weak transcription	Psoas Muscle	Psoas
28	chr6:71214600-71227800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:71214600-71234600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:71214600-71241600	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:71214600-71244000	Weak transcription	Esophagus	oesophagus
32	chr6:71214600-71244400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:71214600-71248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:71214600-71248600	Weak transcription	NHEK	skin
35	chr6:71214600-71248800	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:71214600-71251200	Weak transcription	K562	blood
37	chr6:71214600-71276000	Weak transcription	A549	lung
38	chr6:71214800-71240400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:71215000-71226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:71215000-71273000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:71215200-71224000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:71215200-71224000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:71215200-71224200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:71215200-71224200	Weak transcription	Adipose Nuclei	Adipose
45	chr6:71215200-71234600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:71216000-71232400	Weak transcription	Placenta	Placenta
47	chr6:71216000-71240400	Weak transcription	GM12878-XiMat	blood
48	chr6:71216200-71224400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:71216200-71233400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:71216200-71233600	Weak transcription	Monocytes-CD14+_RO01746	blood

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