Variant report

Variant	rs6828858
Chromosome Location	chr4:7774064-7774065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7754937..7756768-chr4:7773872..7775799,2	K562	blood:
2	chr4:7768892..7770809-chr4:7771728..7774160,2	K562	blood:
3	chr4:7763518..7765099-chr4:7771981..7774242,3	K562	blood:
4	chr4:7773384..7775813-chr4:7806131..7807839,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SORCS2-1	chr4:7773931-7776364	NONHSAT095064

Variant related genes	Relation type
ENSG00000272620	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10009045	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018256	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12639946	0.81[EUR][1000 genomes]
rs2067842	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3934540	0.91[EUR][1000 genomes]
rs4234831	0.91[EUR][1000 genomes]
rs4443285	0.91[EUR][1000 genomes]
rs4447865	0.91[EUR][1000 genomes]
rs4579115	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4689860	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4689865	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689875	0.84[EUR][1000 genomes]
rs6446624	0.91[EUR][1000 genomes]
rs6446625	0.84[EUR][1000 genomes]
rs6829710	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6856371	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6856795	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71612280	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7654361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7682611	0.81[EUR][1000 genomes]
rs7684718	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9996019	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
2	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
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats 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	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7757600-7779600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr4:7758000-7780800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
5	chr4:7758600-7780600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
7	chr4:7760000-7783000	Strong transcription	HSMMtube	muscle
8	chr4:7760000-7783200	Strong transcription	HSMM	muscle
9	chr4:7760200-7774200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:7760200-7779400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:7760400-7780400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:7760600-7780000	Weak transcription	Right Atrium	heart
13	chr4:7761000-7780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:7761200-7781000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:7761800-7774400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
19	chr4:7763000-7775400	Weak transcription	Right Ventricle	heart
20	chr4:7764000-7774400	Strong transcription	Adipose Nuclei	Adipose
21	chr4:7764400-7776400	Strong transcription	Gastric	stomach
22	chr4:7764800-7774400	Strong transcription	Placenta	Placenta
23	chr4:7765000-7776600	Strong transcription	Spleen	Spleen
24	chr4:7765000-7780000	Strong transcription	Lung	lung
25	chr4:7766000-7780600	Strong transcription	Osteobl	bone
26	chr4:7766800-7781200	Strong transcription	HUVEC	blood vessel
27	chr4:7767200-7776600	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr4:7767200-7780800	Strong transcription	NH-A	brain
29	chr4:7767600-7781000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr4:7767800-7774600	Genic enhancers	Stomach Smooth Muscle	stomach
31	chr4:7768000-7774400	Strong transcription	NHDF-Ad	bronchial
32	chr4:7768200-7776200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:7768200-7777200	Weak transcription	Brain Substantia Nigra	brain
34	chr4:7768400-7775400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr4:7769000-7780200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:7769200-7776400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:7770000-7775600	Genic enhancers	Fetal Stomach	stomach
38	chr4:7770200-7776200	Strong transcription	Fetal Lung	lung
39	chr4:7770400-7774600	Strong transcription	Esophagus	oesophagus
40	chr4:7770400-7776800	Strong transcription	Aorta	Aorta
41	chr4:7770800-7774400	Weak transcription	Small Intestine	intestine
42	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr4:7771200-7776600	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr4:7771200-7777200	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:7771600-7775400	Genic enhancers	HepG2	liver
46	chr4:7771600-7780800	Strong transcription	Pancreas	Pancrea
47	chr4:7771800-7780200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:7772000-7776000	Genic enhancers	Fetal Intestine Large	intestine
49	chr4:7772000-7776000	Genic enhancers	Fetal Intestine Small	intestine
50	chr4:7772000-7783000	Weak transcription	Primary monocytes fromperipheralblood	blood

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