Variant report

Variant	rs1922722
Chromosome Location	chr7:66174961-66174962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10950047	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11763224	0.82[EUR][1000 genomes]
rs11766583	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12666079	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667394	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1267814	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13311962	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1638724	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1638725	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1638728	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1638732	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1638735	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796212	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796217	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796218	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796219	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796222	0.82[EUR][1000 genomes]
rs1796226	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796227	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862085	0.82[EUR][1000 genomes]
rs2052089	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420612	0.84[EUR][1000 genomes]
rs2533282	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2533283	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2533284	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2707851	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28425729	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28817617	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2901267	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3800815	0.83[ASN][1000 genomes]
rs4717322	0.81[ASN][1000 genomes]
rs4718364	0.85[EUR][1000 genomes]
rs4718385	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718410	0.81[ASN][1000 genomes]
rs6460311	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6947441	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6961853	0.85[EUR][1000 genomes]
rs6966953	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6970767	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6979167	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73139927	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73139974	0.81[ASN][1000 genomes]
rs73152714	0.85[EUR][1000 genomes]
rs73377549	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73377594	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801199	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs801210	0.91[EUR][1000 genomes]
rs801212	0.91[EUR][1000 genomes]
rs801213	0.91[EUR][1000 genomes]
rs964971	0.91[EUR][1000 genomes];0.85[ASN][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	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1922722	GS1-124K5.11	cis	Thyroid	GTEx
rs1922722	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs1922722	RNU6-96P	cis	Thyroid	GTEx
rs1922722	GS1-124K5.4	cis	Stomach	GTEx
rs1922722	GS1-124K5.4	cis	Artery Aorta	GTEx
rs1922722	GTF2IRD1P1	cis	Thyroid	GTEx
rs1922722	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66148000-66177600	Weak transcription	Aorta	Aorta
2	chr7:66148200-66175600	Weak transcription	Primary B cells from cord blood	blood
3	chr7:66148400-66178400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:66148400-66182400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr7:66148400-66184400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:66148400-66184800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:66148600-66177400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:66149000-66177600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:66149000-66199600	Weak transcription	Thymus	Thymus
10	chr7:66149600-66178400	Weak transcription	GM12878-XiMat	blood
11	chr7:66149600-66190200	Weak transcription	Hela-S3	cervix
12	chr7:66151400-66178400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:66153400-66178400	Weak transcription	Fetal Kidney	kidney
14	chr7:66153400-66182200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr7:66154200-66177400	Weak transcription	Fetal Intestine Large	intestine
16	chr7:66155200-66178400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:66158000-66177200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr7:66159000-66180000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr7:66159200-66175400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:66159400-66180000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:66159600-66178000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:66159600-66178400	Weak transcription	Primary T cells from cord blood	blood
23	chr7:66159600-66190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:66159800-66177800	Weak transcription	HSMMtube	muscle
25	chr7:66159800-66180800	Weak transcription	Brain Germinal Matrix	brain
26	chr7:66160000-66177400	Weak transcription	Liver	Liver
27	chr7:66162200-66177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:66162400-66177600	Weak transcription	Placenta	Placenta
29	chr7:66162400-66189400	Weak transcription	Psoas Muscle	Psoas
30	chr7:66162600-66175800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:66162600-66177400	Weak transcription	NHLF	lung
32	chr7:66162600-66178400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:66162600-66178400	Weak transcription	NHEK	skin
34	chr7:66162600-66180600	Weak transcription	HMEC	breast
35	chr7:66162600-66192400	Weak transcription	NH-A	brain
36	chr7:66162600-66196800	Weak transcription	Right Ventricle	heart
37	chr7:66162800-66177600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:66163000-66175000	Weak transcription	HSMM	muscle
39	chr7:66163000-66190800	Weak transcription	Esophagus	oesophagus
40	chr7:66163400-66178400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:66163600-66178400	Weak transcription	Fetal Brain Male	brain
42	chr7:66164000-66180800	Weak transcription	HepG2	liver
43	chr7:66164400-66177400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr7:66165200-66189800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:66165400-66177400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:66165400-66177400	Weak transcription	Fetal Muscle Leg	muscle
47	chr7:66165400-66177600	Weak transcription	Brain Anterior Caudate	brain
48	chr7:66165400-66182400	Weak transcription	Left Ventricle	heart
49	chr7:66165400-66188600	Weak transcription	Lung	lung
50	chr7:66165400-66204600	Weak transcription	Rectal Smooth Muscle	rectum

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