Variant report

Variant	rs4689858
Chromosome Location	chr4:7775587-7775588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7770767..7773381-chr4:7774826..7777247,2	K562	blood:
2	chr4:7754937..7756768-chr4:7773872..7775799,2	K562	blood:
3	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: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10000569	0.83[ASN][1000 genomes]
rs10004558	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022249	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025396	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031989	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050114	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155361	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10937858	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937860	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10937862	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11944501	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501412	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503512	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508657	0.81[AMR][1000 genomes]
rs16841116	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841207	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406288	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28429656	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28726367	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28735524	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28759100	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689857	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689861	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6856818	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73206599	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73208810	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356232	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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:111 , 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	chr4:7760200-7779400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:7760400-7780400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:7760600-7780000	Weak transcription	Right Atrium	heart
12	chr4:7761000-7780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:7761200-7781000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
17	chr4:7764400-7776400	Strong transcription	Gastric	stomach
18	chr4:7765000-7776600	Strong transcription	Spleen	Spleen
19	chr4:7765000-7780000	Strong transcription	Lung	lung
20	chr4:7766000-7780600	Strong transcription	Osteobl	bone
21	chr4:7766800-7781200	Strong transcription	HUVEC	blood vessel
22	chr4:7767200-7776600	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr4:7767200-7780800	Strong transcription	NH-A	brain
24	chr4:7767600-7781000	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr4:7768200-7776200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:7768200-7777200	Weak transcription	Brain Substantia Nigra	brain
27	chr4:7769000-7780200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:7769200-7776400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:7770000-7775600	Genic enhancers	Fetal Stomach	stomach
30	chr4:7770200-7776200	Strong transcription	Fetal Lung	lung
31	chr4:7770400-7776800	Strong transcription	Aorta	Aorta
32	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr4:7771200-7776600	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:7771200-7777200	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:7771600-7780800	Strong transcription	Pancreas	Pancrea
36	chr4:7771800-7780200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:7772000-7776000	Genic enhancers	Fetal Intestine Large	intestine
38	chr4:7772000-7776000	Genic enhancers	Fetal Intestine Small	intestine
39	chr4:7772000-7783000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:7772400-7776600	Strong transcription	Brain Germinal Matrix	brain
41	chr4:7772600-7776400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:7772800-7775800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr4:7772800-7778800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:7772800-7780400	Weak transcription	Brain Angular Gyrus	brain
45	chr4:7773000-7776600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:7773000-7776600	Strong transcription	Fetal Brain Female	brain
47	chr4:7773200-7775600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
48	chr4:7773200-7776600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:7773200-7777000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:7773400-7775600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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