Variant report

Variant	rs55815340
Chromosome Location	chr1:176174324-176174325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:176174148-176174977	K562	blood:	n/a	chr1:176174707-176174720 chr1:176174708-176174722
2	CUX1	chr1:176174130-176175104	K562	blood:	n/a	chr1:176174549-176174558

No.	Distal block	Cell Line	Cell type
1	chr1:176159070..176161362-chr1:176173225..176174837,2	K562	blood:
2	chr1:176165919..176170805-chr1:176171085..176174433,5	K562	blood:
3	chr1:176173011..176175241-chr1:176190207..176192824,3	K562	blood:
4	chr1:176153551..176156175-chr1:176174165..176176640,2	K562	blood:
5	chr1:176152065..176154740-chr1:176172886..176175167,2	MCF-7	breast:
6	chr1:176163691..176165683-chr1:176171468..176174461,2	K562	blood:

Variant related genes	Relation type
ENSG00000236021	TF binding region
ENSG00000143207	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12402588	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12403164	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12408191	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409154	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16849609	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17354043	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4265393	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4498761	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56346636	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57729493	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58539711	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs59540069	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59801736	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60630667	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61820962	0.85[AMR][1000 genomes]
rs61820963	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61820964	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61820966	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61820969	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61820971	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61820976	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821005	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821006	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821032	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821033	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821035	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821055	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61821058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61821059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61822660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61822661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61822663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61822765	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61822766	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61822768	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs74127162	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7553673	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
2	chr1:176166000-176175400	Weak transcription	Spleen	Spleen
3	chr1:176168800-176174600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:176169600-176174400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:176171200-176174400	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:176171600-176175200	Weak transcription	Gastric	stomach
7	chr1:176171600-176175400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:176171800-176175200	Weak transcription	Lung	lung
9	chr1:176172400-176174600	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:176172400-176174800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr1:176172800-176174400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:176173000-176174400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:176173000-176174400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:176173000-176174400	Enhancers	Liver	Liver
15	chr1:176173000-176174400	Enhancers	Fetal Lung	lung
16	chr1:176173000-176174600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:176173000-176174600	Enhancers	Fetal Heart	heart
18	chr1:176173000-176174600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:176173000-176174600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:176173000-176174800	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:176173000-176175200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr1:176173000-176175200	Flanking Active TSS	Dnd41	blood
23	chr1:176173200-176174400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:176173200-176174400	Weak transcription	Aorta	Aorta
25	chr1:176173200-176174600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:176173400-176174400	Enhancers	Fetal Thymus	thymus
27	chr1:176173400-176174800	Weak transcription	Fetal Stomach	stomach
28	chr1:176173400-176175400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr1:176173600-176174400	Flanking Active TSS	GM12878-XiMat	blood
30	chr1:176173600-176174600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:176173600-176174800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:176173600-176174800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:176173600-176175000	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr1:176173600-176175800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr1:176173600-176175800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:176173600-176176000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr1:176173800-176174400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:176173800-176174400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr1:176173800-176174400	Enhancers	Placenta	Placenta
40	chr1:176173800-176174400	Enhancers	Stomach Smooth Muscle	stomach
41	chr1:176173800-176174600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:176173800-176174800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:176173800-176174800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr1:176173800-176174800	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr1:176173800-176175000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:176173800-176175000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:176173800-176175400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:176173800-176175800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:176173800-176177600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:176173800-176177600	Active TSS	HSMM	muscle

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