Variant report

Variant	rs4610622
Chromosome Location	chr7:66224497-66224498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66220562..66222668-chr7:66223187..66225396,2	K562	blood:

Variant related genes	Relation type
ENSG00000154710	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1016265	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10233806	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10244498	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10274883	0.83[AFR][1000 genomes]
rs10950049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950050	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11761542	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11772819	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13226966	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13308803	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1544549	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1860469	0.84[AFR][1000 genomes]
rs1860472	0.82[AFR][1000 genomes]
rs1962050	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003300	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2013908	0.82[AFR][1000 genomes]
rs2109297	0.83[AFR][1000 genomes]
rs2420820	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2659890	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2659891	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2659892	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2659893	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2659894	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659895	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659896	0.81[AMR][1000 genomes]
rs2659897	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659898	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2659900	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659901	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2659904	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659907	0.86[AFR][1000 genomes]
rs2659908	0.86[AFR][1000 genomes]
rs2659914	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2707824	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2707837	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2707839	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2707847	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28480509	0.83[AFR][1000 genomes]
rs3857687	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4717315	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4718383	0.84[AFR][1000 genomes]
rs58347342	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs66981195	0.82[AFR][1000 genomes]
rs6951302	0.84[AFR][1000 genomes]
rs6958200	0.89[EUR][1000 genomes]
rs6969679	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6975044	0.89[AFR][1000 genomes]
rs6978178	0.83[AFR][1000 genomes]
rs721717	0.84[AFR][1000 genomes]
rs7782587	0.83[AFR][1000 genomes]
rs7800620	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7805152	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs881285	0.81[AFR][1000 genomes]
rs974239	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791712	0.84[AFR][1000 genomes]
rs9791713	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv981512	chr7:66223352-66249901	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4610622	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs4610622	GS1-124K5.4	cis	Artery Aorta	GTEx
rs4610622	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs4610622	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs4610622	GS1-124K5.4	cis	Stomach	GTEx
rs4610622	RNU6-96P	cis	Thyroid	GTEx
rs4610622	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs4610622	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs4610622	GTF2IRD1P1	cis	Thyroid	GTEx
rs4610622	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs4610622	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs4610622	RP4-756H11.3	cis	Artery Aorta	GTEx
rs4610622	GS1-124K5.11	cis	Thyroid	GTEx
rs4610622	RP4-756H11.3	cis	Artery Tibial	GTEx
rs4610622	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4610622	RP4-756H11.3	cis	Thyroid	GTEx
rs4610622	RP4-756H11.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66206800-66232600	Weak transcription	Primary T cells from cord blood	blood
2	chr7:66206800-66238800	Weak transcription	Aorta	Aorta
3	chr7:66207000-66227400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:66207000-66227400	Weak transcription	Fetal Stomach	stomach
5	chr7:66207000-66230600	Weak transcription	Fetal Intestine Large	intestine
6	chr7:66207000-66230600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr7:66207000-66234000	Weak transcription	Fetal Thymus	thymus
8	chr7:66207000-66238400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:66207000-66238400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:66207600-66239800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:66207800-66225800	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:66208000-66230600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:66208000-66232400	Weak transcription	Thymus	Thymus
15	chr7:66208000-66236800	Weak transcription	Dnd41	blood
16	chr7:66208000-66238000	Weak transcription	A549	lung
17	chr7:66208000-66238600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:66208000-66238600	Weak transcription	Brain Germinal Matrix	brain
19	chr7:66208000-66240800	Weak transcription	HSMMtube	muscle
20	chr7:66208000-66241800	Weak transcription	Hela-S3	cervix
21	chr7:66209400-66239000	Weak transcription	HMEC	breast
22	chr7:66211000-66228600	Weak transcription	Fetal Lung	lung
23	chr7:66212000-66236800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:66213200-66234400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:66213400-66230600	Weak transcription	NH-A	brain
26	chr7:66214200-66225800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:66214200-66234200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr7:66214400-66225000	Weak transcription	Ovary	ovary
29	chr7:66214400-66229600	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:66214400-66234200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:66214400-66236600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:66214400-66239400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr7:66214600-66231000	Weak transcription	Left Ventricle	heart
34	chr7:66214600-66234000	Weak transcription	NHLF	lung
35	chr7:66214600-66234200	Weak transcription	Gastric	stomach
36	chr7:66215000-66230600	Weak transcription	Fetal Intestine Small	intestine
37	chr7:66215600-66234200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr7:66215800-66234200	Weak transcription	NHEK	skin
39	chr7:66216800-66239400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr7:66220000-66241000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr7:66220800-66228400	Weak transcription	Brain Substantia Nigra	brain
42	chr7:66220800-66229600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr7:66220800-66230800	Weak transcription	Brain Angular Gyrus	brain
44	chr7:66221600-66229800	Weak transcription	Fetal Heart	heart
45	chr7:66221800-66240400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:66222400-66228400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:66222800-66224600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:66222800-66228000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:66223000-66225200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr7:66223200-66224600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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