Variant report

Variant	rs632430
Chromosome Location	chr6:140248121-140248122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140242464..140245824-chr6:140246316..140249558,3	K562	blood:
2	chr6:140247524..140250315-chr6:140258612..140260750,2	K562	blood:
3	chr6:139693225..139698326-chr6:140245231..140252808,11	MCF-7	breast:
4	chr6:140246862..140249416-chr6:140250072..140252711,2	K562	blood:
5	chr6:139692080..139697357-chr6:140246933..140251926,6	MCF-7	breast:
6	chr6:140247244..140249348-chr6:140253799..140256796,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1572671	0.81[EUR][1000 genomes]
rs4896494	0.86[JPT][hapmap]
rs590585	0.82[CHB][hapmap]
rs591269	0.85[ASN][1000 genomes]
rs613274	0.86[CHB][hapmap]
rs618471	0.81[CHB][hapmap]
rs642162	0.86[JPT][hapmap]
rs661063	0.80[ASN][1000 genomes]
rs6921044	0.81[EUR][1000 genomes]
rs9321762	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs632430	LTV1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140239800-140251600	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:140242400-140254000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:140242400-140260200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:140242800-140254400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:140245000-140249000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:140246000-140249400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:140246400-140248200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:140246400-140249400	Enhancers	NHDF-Ad	bronchial
9	chr6:140246600-140248200	Enhancers	Fetal Intestine Small	intestine
10	chr6:140246600-140248600	Enhancers	Fetal Intestine Large	intestine
11	chr6:140246600-140249400	Enhancers	NHLF	lung
12	chr6:140246800-140248200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:140246800-140249200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:140247000-140248200	Enhancers	Fetal Brain Male	brain
15	chr6:140247000-140248400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:140247200-140248200	Enhancers	Duodenum Mucosa	Duodenum
17	chr6:140247200-140248200	Enhancers	Fetal Muscle Leg	muscle
18	chr6:140247200-140248200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:140247200-140248200	Flanking Active TSS	HSMMtube	muscle
20	chr6:140247200-140248200	Flanking Active TSS	Osteobl	bone
21	chr6:140247200-140248400	Enhancers	Ovary	ovary
22	chr6:140247200-140248800	Enhancers	Fetal Brain Female	brain
23	chr6:140247200-140250000	Enhancers	K562	blood
24	chr6:140247600-140248200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:140247600-140248200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr6:140247600-140248200	Enhancers	Pancreas	Pancrea
27	chr6:140247600-140248200	Enhancers	HepG2	liver
28	chr6:140247600-140248600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr6:140247800-140248800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:140247800-140250000	Enhancers	Fetal Heart	heart
31	chr6:140248000-140248600	Enhancers	Stomach Smooth Muscle	stomach
32	chr6:140248000-140248600	Enhancers	NH-A	brain
33	chr6:140248000-140248800	Enhancers	HSMM	muscle
34	chr6:140248000-140249200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:140248000-140249400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:140248000-140249600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:140248000-140252400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:140248000-140252800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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