Variant report

Variant	rs41300963
Chromosome Location	chr1:213061050-213061051
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	chr1:213055380..213057887-chr1:213059654..213061319,2	K562	blood:

Variant related genes	Relation type
ENSG00000162769	Chromatin interaction

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

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

rs_ID	r²[population]
rs11799556	1.00[AMR][1000 genomes]
rs11801740	1.00[EUR][1000 genomes]
rs11801900	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11804851	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11807916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17019640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17019657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17019749	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17019770	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17020130	1.00[AMR][1000 genomes]
rs28505349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41296716	1.00[EUR][1000 genomes]
rs55787749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55827218	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56012560	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60267007	1.00[EUR][1000 genomes]
rs6675972	1.00[EUR][1000 genomes]
rs6684313	1.00[AMR][1000 genomes]
rs6685348	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6700258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138631	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74138700	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140504	1.00[EUR][1000 genomes]
rs74140506	1.00[EUR][1000 genomes]
rs74140507	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140511	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7511916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7523527	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7538679	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7551472	1.00[AMR][1000 genomes]
rs7551969	1.00[AMR][1000 genomes];1.00[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	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1007129	chr1:213037244-213083261	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213032600-213073000	Weak transcription	Colonic Mucosa	Colon
2	chr1:213032600-213073000	Weak transcription	Esophagus	oesophagus
3	chr1:213032800-213061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:213032800-213062000	Weak transcription	Psoas Muscle	Psoas
5	chr1:213033600-213062000	Weak transcription	Thymus	Thymus
6	chr1:213034400-213068000	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:213034600-213061800	Weak transcription	Fetal Heart	heart
8	chr1:213034600-213067800	Weak transcription	NHLF	lung
9	chr1:213034600-213070600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:213035800-213073000	Weak transcription	Small Intestine	intestine
11	chr1:213036000-213070800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:213036200-213062000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:213036400-213062000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:213037600-213073200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:213038400-213072000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:213039600-213073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:213040400-213073000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:213043200-213062000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:213043200-213073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:213044400-213063200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:213045000-213070800	Weak transcription	Pancreas	Pancrea
22	chr1:213046600-213066400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:213047000-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:213047200-213061800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:213047200-213062000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:213048800-213062600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:213049000-213061800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:213049000-213073000	Weak transcription	HSMMtube	muscle
29	chr1:213049400-213063200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:213049600-213062000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:213049800-213061800	Weak transcription	Ovary	ovary
32	chr1:213049800-213062000	Weak transcription	Gastric	stomach
33	chr1:213049800-213062600	Weak transcription	NHEK	skin
34	chr1:213049800-213072400	Weak transcription	Fetal Brain Male	brain
35	chr1:213049800-213073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:213049800-213073200	Weak transcription	Spleen	Spleen
37	chr1:213050000-213065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:213050800-213065800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:213051200-213064400	Strong transcription	Hela-S3	cervix
40	chr1:213052200-213073000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:213052600-213066000	Strong transcription	HepG2	liver
42	chr1:213052800-213062200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:213052800-213073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:213053200-213066200	Strong transcription	Dnd41	blood
45	chr1:213053400-213073800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:213053600-213073000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:213053800-213073200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:213053800-213073200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:213054000-213071000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:213054200-213071400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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