Variant report

Variant	rs2420821
Chromosome Location	chr7:66097333-66097334
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66096656..66098243-chr7:66117649..66119984,2	K562	blood:
2	chr7:66091898..66097382-chr7:66117985..66122507,10	K562	blood:
3	chr7:66091920..66094757-chr7:66096200..66098462,2	K562	blood:

Variant related genes	Relation type
ENSG00000226824	Chromatin interaction
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10274883	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10278014	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11772884	0.81[AMR][1000 genomes]
rs12333370	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13240501	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13242290	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13308803	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1860469	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1860472	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1968126	0.80[AMR][1000 genomes]
rs2013908	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2024192	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2109297	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2659890	0.80[EUR][1000 genomes]
rs2659891	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659892	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659893	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659898	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2659901	0.80[EUR][1000 genomes]
rs2659907	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2659908	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2707824	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2707847	0.80[EUR][1000 genomes]
rs28480509	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3846973	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3926380	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4506088	0.83[AMR][1000 genomes]
rs4717315	0.80[EUR][1000 genomes]
rs4718377	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4718383	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66981195	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6951302	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6951946	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6955837	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6971059	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6973249	0.90[AMR][1000 genomes]
rs6978178	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs721717	0.85[AMR][1000 genomes]
rs7384021	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7385102	0.85[AMR][1000 genomes]
rs7782587	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7793723	0.84[AMR][1000 genomes]
rs7808013	0.82[EUR][1000 genomes]
rs801194	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs881285	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9791712	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9791713	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS 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	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv2761151	chr7:66095738-66138285	Flanking Active TSS Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2420821	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2420821	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2420821	RP4-756H11.3	cis	lung	GTEx
rs2420821	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs2420821	RP4-756H11.3	cis	Artery Tibial	GTEx
rs2420821	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs2420821	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2420821	GS1-124K5.11	cis	Thyroid	GTEx
rs2420821	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs2420821	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs2420821	GTF2IRD1P1	cis	Thyroid	GTEx
rs2420821	RNU6-96P	cis	Thyroid	GTEx
rs2420821	LINC00174	cis	Thyroid	GTEx
rs2420821	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs2420821	GS1-124K5.2	cis	Whole Blood	GTEx
rs2420821	RP4-756H11.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66094400-66103200	Weak transcription	Small Intestine	intestine
2	chr7:66094600-66097800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:66094800-66097600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr7:66094800-66097800	Enhancers	Primary hematopoietic stem cells	blood
5	chr7:66094800-66098200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:66094800-66098400	Enhancers	Primary B cells from peripheral blood	blood
7	chr7:66094800-66103400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:66095000-66097600	Enhancers	Dnd41	blood
9	chr7:66095000-66098000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:66095000-66098000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:66095000-66098200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:66095000-66098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:66095000-66098200	Weak transcription	Ovary	ovary
14	chr7:66095000-66098200	Weak transcription	HSMMtube	muscle
15	chr7:66095000-66098400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:66095000-66099200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:66095000-66099400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:66095000-66099400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:66095000-66099400	Weak transcription	Aorta	Aorta
20	chr7:66095000-66099600	Weak transcription	A549	lung
21	chr7:66095000-66101000	Weak transcription	NHEK	skin
22	chr7:66095000-66102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:66095000-66103000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:66095000-66103000	Weak transcription	Fetal Kidney	kidney
25	chr7:66095000-66103000	Weak transcription	Fetal Lung	lung
26	chr7:66095000-66103200	Weak transcription	Psoas Muscle	Psoas
27	chr7:66095000-66103400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr7:66095000-66103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:66095000-66103400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr7:66095000-66104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr7:66095000-66108800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr7:66095000-66109000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr7:66095000-66115200	Weak transcription	HMEC	breast
34	chr7:66095200-66098000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:66095200-66098000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:66095200-66098000	Weak transcription	Fetal Intestine Small	intestine
37	chr7:66095200-66098200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:66095200-66098200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:66095200-66098200	Weak transcription	Fetal Intestine Large	intestine
40	chr7:66095200-66098400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr7:66095200-66098600	Weak transcription	Liver	Liver
42	chr7:66095200-66099000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:66095200-66099400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr7:66095200-66099400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:66095200-66099800	Weak transcription	Colonic Mucosa	Colon
46	chr7:66095200-66101000	Weak transcription	NHDF-Ad	bronchial
47	chr7:66095200-66103000	Weak transcription	Stomach Mucosa	stomach
48	chr7:66095200-66103200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:66095200-66118400	Weak transcription	Fetal Heart	heart
50	chr7:66095200-66118400	Weak transcription	HUVEC	blood vessel

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