Variant report

Variant	rs60039374
Chromosome Location	chr1:227466598-227466599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227461718..227464574-chr1:227466542..227468149,2	K562	blood:
2	chr1:227461159..227463186-chr1:227466378..227468211,2	MCF-7	breast:
3	chr1:227465837..227468311-chr1:227473296..227476222,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF678-5	chr1:227466303-227468235	l_204_chr1:227466302-227471954_brain

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11807166	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807511	1.00[AMR][1000 genomes]
rs11807555	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11807766	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808055	1.00[EUR][1000 genomes]
rs11808370	1.00[EUR][1000 genomes]
rs11808613	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11810417	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1355816	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847506	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35099852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4364839	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57660509	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57717956	1.00[EUR][1000 genomes]
rs57895961	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58077821	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59396012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59523055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60423930	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60906739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61494318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61588040	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688385	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6696713	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6699740	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73086744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090609	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090689	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092512	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094358	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094365	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094366	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094390	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73096314	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098350	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73098391	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100303	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102326	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73102327	1.00[EUR][1000 genomes]
rs73102341	1.00[EUR][1000 genomes]
rs73102913	1.00[AMR][1000 genomes]
rs73102948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74143320	1.00[AMR][1000 genomes];1.00[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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3453491	chr1:227462942-227482283	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3453492	chr1:227462956-227482280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
2	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
3	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:227449600-227473600	Weak transcription	NH-A	brain
7	chr1:227453000-227468600	Weak transcription	Lung	lung
8	chr1:227454200-227470400	Weak transcription	Ovary	ovary
9	chr1:227456600-227468800	Weak transcription	Left Ventricle	heart
10	chr1:227458600-227469400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:227458800-227472200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227459400-227469400	Weak transcription	NHEK	skin
13	chr1:227462600-227473600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:227463000-227473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:227464400-227468000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:227464400-227469000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:227464400-227472800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:227464400-227472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:227464600-227468600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:227464600-227468600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:227464600-227469400	Weak transcription	Gastric	stomach
23	chr1:227465400-227472200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:227465600-227468600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:227466000-227468600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:227466000-227468800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:227466200-227473200	Weak transcription	A549	lung

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