Variant report

Variant	rs10020169
Chromosome Location	chr4:8069405-8069406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3TC1-2	chr4:8068787-8069451	ENSG00000251460.1

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10020078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841640	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28416479	1.00[ASN][1000 genomes]
rs28535319	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28588651	0.88[AFR][1000 genomes]
rs4696741	1.00[ASN][1000 genomes]
rs55932143	1.00[ASN][1000 genomes]
rs56192722	1.00[ASN][1000 genomes]
rs57007308	1.00[ASN][1000 genomes]
rs57147516	1.00[ASN][1000 genomes]
rs58061467	1.00[ASN][1000 genomes]
rs58454418	1.00[ASN][1000 genomes]
rs58733360	1.00[ASN][1000 genomes]
rs59070213	1.00[ASN][1000 genomes]
rs59525928	1.00[ASN][1000 genomes]
rs60624370	1.00[ASN][1000 genomes]
rs73074034	1.00[ASN][1000 genomes]
rs73074035	1.00[ASN][1000 genomes]
rs73074036	1.00[ASN][1000 genomes]
rs73074038	1.00[ASN][1000 genomes]
rs73074039	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv829852	chr4:7991906-8151267	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv470009	chr4:8015421-8085174	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv878581	chr4:8021592-8100272	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv878584	chr4:8023484-8075134	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878585	chr4:8023484-8116202	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv878586	chr4:8023484-8148159	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv878587	chr4:8031471-8075134	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv878588	chr4:8034772-8070793	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv878589	chr4:8034772-8089598	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv878590	chr4:8047973-8075134	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv878591	chr4:8063501-8207083	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8060200-8070000	Weak transcription	Brain Angular Gyrus	brain
2	chr4:8060200-8072400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr4:8066200-8070000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:8066600-8070200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:8066600-8071600	Weak transcription	Gastric	stomach
6	chr4:8066800-8071400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:8066800-8075800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:8067000-8070800	Weak transcription	Pancreas	Pancrea
9	chr4:8067000-8072400	Weak transcription	Esophagus	oesophagus
10	chr4:8067400-8072600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:8068400-8069600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
12	chr4:8068800-8069600	Enhancers	Right Ventricle	heart
13	chr4:8068800-8071000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr4:8068800-8071400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:8069000-8069800	Enhancers	Psoas Muscle	Psoas
16	chr4:8069000-8069800	Enhancers	Right Atrium	heart
17	chr4:8069000-8070000	Enhancers	Left Ventricle	heart
18	chr4:8069000-8071000	Enhancers	Fetal Muscle Leg	muscle
19	chr4:8069200-8070200	Strong transcription	Aorta	Aorta
20	chr4:8069200-8070800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr4:8069200-8071400	Strong transcription	Spleen	Spleen
22	chr4:8069400-8070600	Bivalent Enhancer	HepG2	liver

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