Variant report

Variant	rs6083010
Chromosome Location	chr20:23109202-23109203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23088338..23089890-chr20:23107180..23109300,2	MCF-7	breast:
2	chr20:23103723..23106528-chr20:23107935..23111054,5	K562	blood:
3	chr20:23108883..23111876-chr20:23111933..23114373,2	MCF-7	breast:
4	chr20:23103623..23110911-chr20:23111294..23114699,12	K562	blood:
5	chr20:23102012..23106528-chr20:23108448..23111067,5	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSTR4-12	chr20:23109048-23110176	l_2091_chr20:23108768-23110176_testes

No data

Variant related genes	Relation type
ENSG00000233746	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13045861	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6083012	0.92[CEU][hapmap];0.91[AMR][1000 genomes]
rs6083013	0.86[CHB][hapmap]
rs6083014	0.88[CEU][hapmap]
rs6083015	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs6132568	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137837	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs844828	0.83[EUR][1000 genomes]
rs844829	0.83[EUR][1000 genomes]
rs844903	0.86[CHB][hapmap]
rs946369	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs946371	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6083010	LMCD1	trans	lymphoblastoid	seeQTL
rs6083010	RIN2	cis	parietal	SCAN
rs6083010	CST9	cis	cerebellum	SCAN
rs6083010	CST8	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23085800-23114600	Enhancers	Placenta	Placenta
2	chr20:23097600-23110200	Weak transcription	Pancreas	Pancrea
3	chr20:23100200-23111200	Enhancers	Fetal Thymus	thymus
4	chr20:23101200-23109400	Weak transcription	Liver	Liver
5	chr20:23102000-23114000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:23103200-23109800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr20:23104600-23111600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr20:23105000-23109800	Enhancers	Brain Hippocampus Middle	brain
9	chr20:23105200-23111000	Enhancers	Fetal Muscle Leg	muscle
10	chr20:23105800-23110000	Enhancers	Primary B cells from cord blood	blood
11	chr20:23105800-23110000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:23105800-23111000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr20:23106000-23112000	Enhancers	Adipose Nuclei	Adipose
14	chr20:23106200-23110200	Weak transcription	Fetal Intestine Small	intestine
15	chr20:23106400-23109600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr20:23106600-23109800	Weak transcription	Right Atrium	heart
17	chr20:23106600-23111000	Enhancers	Spleen	Spleen
18	chr20:23106600-23112600	Weak transcription	Fetal Intestine Large	intestine
19	chr20:23106800-23109800	Weak transcription	Colonic Mucosa	Colon
20	chr20:23106800-23110800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr20:23106800-23114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr20:23106800-23116400	Weak transcription	Esophagus	oesophagus
23	chr20:23107200-23110800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr20:23107600-23110000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr20:23107600-23110000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr20:23107600-23111200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr20:23107600-23113200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr20:23107800-23111000	Enhancers	Dnd41	blood
29	chr20:23108000-23109400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:23108000-23110000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr20:23108000-23111000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr20:23108200-23109600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr20:23108200-23110000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr20:23108200-23110600	Weak transcription	Psoas Muscle	Psoas
35	chr20:23108400-23109400	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr20:23108600-23109600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr20:23108600-23109600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr20:23108600-23109800	Enhancers	Brain Substantia Nigra	brain
39	chr20:23108800-23109800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr20:23108800-23110400	Enhancers	Primary T cells from cord blood	blood
41	chr20:23108800-23111200	Enhancers	Left Ventricle	heart
42	chr20:23109000-23109400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr20:23109000-23109400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr20:23109000-23110200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr20:23109000-23120200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr20:23109200-23110000	Enhancers	Duodenum Mucosa	Duodenum
47	chr20:23109200-23110000	Enhancers	Fetal Lung	lung
48	chr20:23109200-23110600	Enhancers	Fetal Heart	heart
49	chr20:23109200-23111000	Enhancers	Right Ventricle	heart
50	chr20:23109200-23111400	Enhancers	Lung	lung

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