Variant report

Variant	rs817438
Chromosome Location	chr1:85641119-85641120
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85637356..85640741-chr1:85640857..85643893,3	K562	blood:
2	chr1:85634992..85636920-chr1:85640465..85642629,2	K562	blood:
3	chr1:85641088..85643211-chr1:85665903..85668389,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf52-2	chr1:85639995-85642563	NONHSAT004238

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1674162	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1674175	1.00[EUR][1000 genomes]
rs17386490	0.87[EUR][1000 genomes]
rs4907025	0.91[EUR][1000 genomes]
rs61769452	0.87[EUR][1000 genomes]
rs61769454	0.85[EUR][1000 genomes]
rs817389	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817390	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817391	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817392	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817393	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817394	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817398	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817399	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817401	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817403	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs817404	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs817411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817422	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs817446	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs817447	1.00[EUR][1000 genomes]
rs817451	1.00[EUR][1000 genomes]
rs817453	1.00[EUR][1000 genomes]
rs817456	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs817457	0.83[EUR][1000 genomes]
rs860140	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85608600-85655200	Weak transcription	Aorta	Aorta
2	chr1:85610400-85647800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85615400-85647600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:85615400-85655200	Weak transcription	Lung	lung
5	chr1:85615600-85654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:85615800-85665800	Weak transcription	Esophagus	oesophagus
7	chr1:85617800-85648000	Weak transcription	Liver	Liver
8	chr1:85619000-85655000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:85619200-85647400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:85619800-85646800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:85621000-85645000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:85624400-85647600	Weak transcription	HSMM	muscle
13	chr1:85625600-85654600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:85626800-85655600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:85627200-85657400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:85627400-85654200	Weak transcription	Gastric	stomach
17	chr1:85627400-85655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:85627400-85663000	Weak transcription	NHEK	skin
19	chr1:85627600-85648000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:85627800-85655800	Weak transcription	NHDF-Ad	bronchial
21	chr1:85627800-85664400	Weak transcription	Osteobl	bone
22	chr1:85628400-85647400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:85628600-85648000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:85629000-85645200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:85629800-85653600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:85630600-85643600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:85630600-85647600	Weak transcription	Adipose Nuclei	Adipose
28	chr1:85630800-85647800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:85630800-85647800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:85631200-85654000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:85631400-85654200	Weak transcription	HepG2	liver
32	chr1:85632000-85648400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:85632600-85647800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:85632800-85647800	Weak transcription	Fetal Lung	lung
35	chr1:85633400-85655000	Weak transcription	Fetal Intestine Small	intestine
36	chr1:85633600-85654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:85633800-85642800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:85634000-85655200	Weak transcription	Fetal Stomach	stomach
39	chr1:85634200-85645200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:85638400-85654800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:85638600-85647400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:85638600-85655200	Weak transcription	Left Ventricle	heart
43	chr1:85638800-85647600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:85639000-85647600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:85639000-85647800	Weak transcription	Fetal Intestine Large	intestine
46	chr1:85639000-85665400	Weak transcription	Placenta	Placenta
47	chr1:85639400-85643000	Weak transcription	K562	blood
48	chr1:85640200-85645200	Weak transcription	Fetal Heart	heart
49	chr1:85640400-85642200	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:85640600-85644200	Weak transcription	Rectal Smooth Muscle	rectum

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