Variant report

Variant	rs61822663
Chromosome Location	chr1:176172833-176172834
allele	A/T
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	EP300	chr1:176172656-176172866	GM12878	blood:	n/a	n/a
2	IRF1	chr1:176172710-176172881	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:176165919..176170805-chr1:176171085..176174433,5	K562	blood:
2	chr1:176170474..176173466-chr1:176174681..176177050,4	K562	blood:
3	chr1:176163691..176165683-chr1:176171468..176174461,2	K562	blood:

Variant related genes	Relation type
ENSG00000236021	TF binding region
ENSG00000236021	Chromatin interaction
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]
rs55815340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
3	chr1:176137400-176173000	Weak transcription	Right Ventricle	heart
4	chr1:176144400-176173400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:176145000-176173200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:176146000-176173000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:176150600-176173000	Weak transcription	Hela-S3	cervix
8	chr1:176151800-176173000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:176152000-176173000	Weak transcription	Thymus	Thymus
10	chr1:176153200-176173000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:176153600-176173000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:176153600-176173000	Weak transcription	HSMM	muscle
13	chr1:176161600-176173800	Weak transcription	HUVEC	blood vessel
14	chr1:176163000-176173400	Weak transcription	Fetal Thymus	thymus
15	chr1:176163600-176173000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:176164200-176173200	Weak transcription	Brain Germinal Matrix	brain
17	chr1:176166000-176173000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:176166000-176175400	Weak transcription	Spleen	Spleen
19	chr1:176166600-176173000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:176166600-176173000	Weak transcription	Right Atrium	heart
21	chr1:176168000-176174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:176168400-176173400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr1:176168800-176173000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:176168800-176174600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:176169000-176173000	Weak transcription	Fetal Intestine Large	intestine
26	chr1:176169000-176173000	Weak transcription	Psoas Muscle	Psoas
27	chr1:176169000-176173000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:176169000-176173800	Weak transcription	Ovary	ovary
29	chr1:176169400-176173000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:176169600-176174400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:176169800-176173000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:176169800-176173000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:176169800-176173000	Weak transcription	Brain Anterior Caudate	brain
34	chr1:176169800-176173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:176169800-176173800	Weak transcription	Brain Angular Gyrus	brain
36	chr1:176169800-176173800	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:176169800-176174200	Weak transcription	Brain Substantia Nigra	brain
38	chr1:176170000-176173000	Weak transcription	Liver	Liver
39	chr1:176170200-176173000	Weak transcription	Primary T cells from cord blood	blood
40	chr1:176170400-176174000	Weak transcription	Fetal Intestine Small	intestine
41	chr1:176170600-176173000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:176170600-176173600	Active TSS	GM12878-XiMat	blood
43	chr1:176170800-176173000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:176171000-176173000	Weak transcription	NHEK	skin
45	chr1:176171000-176173800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:176171200-176173000	Enhancers	Dnd41	blood
47	chr1:176171200-176174400	Enhancers	Primary T cells fromperipheralblood	blood
48	chr1:176171400-176173800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:176171400-176173800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:176171600-176173000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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