Variant report

Variant	rs61820999
Chromosome Location	chr1:176055838-176055839
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:176048905..176051359-chr1:176053995..176056465,2	K562	blood:

Variant related genes	Relation type
ENSG00000143207	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10494499	0.91[AMR][1000 genomes]
rs11576862	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12403794	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12404181	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17351808	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17351933	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17352072	0.91[AMR][1000 genomes]
rs17354252	0.91[AMR][1000 genomes]
rs2481647	0.84[EUR][1000 genomes]
rs2481651	0.86[EUR][1000 genomes]
rs2481657	0.86[EUR][1000 genomes]
rs2502822	0.86[EUR][1000 genomes]
rs2502826	0.86[EUR][1000 genomes]
rs2861630	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4129061	0.86[EUR][1000 genomes]
rs4307526	0.82[EUR][1000 genomes]
rs4314844	0.82[EUR][1000 genomes]
rs4460596	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4601543	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60719126	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60964243	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61186664	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61820953	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61820960	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61820965	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61820968	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61821007	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61821009	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61821028	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61822662	0.91[AMR][1000 genomes]
rs61822767	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6680309	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6693947	0.81[AMR][1000 genomes]
rs6704509	0.82[EUR][1000 genomes]
rs74127150	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs74127154	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74127185	0.88[AMR][1000 genomes]
rs7545639	0.82[EUR][1000 genomes]
rs7554913	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	nsv872564	chr1:176027978-176102808	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548246	chr1:176043797-176136273	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:175994200-176065200	Weak transcription	Psoas Muscle	Psoas
3	chr1:176007800-176066400	Weak transcription	Fetal Brain Male	brain
4	chr1:176010400-176066000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:176012400-176062800	Weak transcription	Lung	lung
6	chr1:176012400-176065800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:176028200-176079200	Weak transcription	HSMMtube	muscle
8	chr1:176035000-176069800	Weak transcription	NHEK	skin
9	chr1:176035200-176067600	Weak transcription	Colonic Mucosa	Colon
10	chr1:176035400-176066400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:176035400-176067200	Weak transcription	HUVEC	blood vessel
12	chr1:176037200-176064600	Weak transcription	Gastric	stomach
13	chr1:176037200-176067200	Weak transcription	Small Intestine	intestine
14	chr1:176037200-176067400	Weak transcription	Osteobl	bone
15	chr1:176038600-176068800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:176038800-176059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:176039200-176068800	Weak transcription	HMEC	breast
18	chr1:176039400-176058800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:176040600-176065400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:176042200-176056600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:176042800-176067200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:176043000-176065400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:176045200-176064600	Weak transcription	Fetal Stomach	stomach
24	chr1:176045800-176066000	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:176046600-176057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:176046600-176082200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:176048400-176064400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:176048400-176067600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:176048600-176063000	Weak transcription	Fetal Lung	lung
30	chr1:176048600-176064800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:176048600-176065600	Weak transcription	A549	lung
32	chr1:176048600-176066400	Weak transcription	Fetal Kidney	kidney
33	chr1:176048800-176057200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:176048800-176062800	Weak transcription	Fetal Thymus	thymus
35	chr1:176048800-176064400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:176048800-176064600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:176048800-176065200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:176048800-176065200	Weak transcription	Brain Germinal Matrix	brain
39	chr1:176048800-176065400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:176048800-176066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:176048800-176107000	Weak transcription	HepG2	liver
42	chr1:176049200-176056600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:176049200-176065200	Weak transcription	Left Ventricle	heart
44	chr1:176049200-176065400	Weak transcription	Thymus	Thymus
45	chr1:176049200-176067200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:176050000-176065200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:176050000-176066000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:176050200-176058200	Weak transcription	Primary T cells from cord blood	blood
49	chr1:176050200-176064400	Weak transcription	Fetal Intestine Large	intestine
50	chr1:176050200-176065800	Weak transcription	Rectal Mucosa Donor 29	rectum

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