Variant report

Variant	rs4743077
Chromosome Location	chr9:100091485-100091486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10122063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10125198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1020884	0.89[EUR][1000 genomes]
rs1020885	0.89[EUR][1000 genomes]
rs1037948	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1037950	0.92[EUR][1000 genomes]
rs1037951	0.88[EUR][1000 genomes]
rs10435867	0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10435868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10448274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759527	0.88[CEU][hapmap]
rs10759624	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759657	0.89[EUR][1000 genomes]
rs10817273	0.89[CEU][hapmap]
rs10817286	0.89[CEU][hapmap]
rs10817487	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981280	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs10981288	0.93[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs10981296	0.87[YRI][hapmap]
rs10981329	0.93[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs10981438	0.84[ASN][1000 genomes]
rs10981890	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10981919	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs10981931	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs11581	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11791310	0.93[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap]
rs12235305	0.84[ASN][1000 genomes]
rs13298346	0.93[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs13299627	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs1542506	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1544203	0.93[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs1903635	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1947717	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2219664	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs2242187	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279114	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306097	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493442	0.81[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2493443	0.85[ASN][1000 genomes]
rs2502644	0.80[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2615143	0.93[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs2615145	0.93[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs2795365	0.86[ASN][1000 genomes]
rs2795367	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs2818238	0.93[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs2818239	0.85[ASN][1000 genomes]
rs2818243	0.86[ASW][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs3214072	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs34955252	0.86[ASN][1000 genomes]
rs35609998	0.86[ASN][1000 genomes]
rs3747489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3747496	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802471	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4237189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4313271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4366181	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4523384	0.86[ASN][1000 genomes]
rs4523385	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4554595	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742685	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742689	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4742690	0.89[EUR][1000 genomes]
rs4743072	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4743076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743087	0.96[CEU][hapmap]
rs4743088	0.96[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6478095	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478131	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7020393	0.86[JPT][hapmap]
rs7042707	0.86[JPT][hapmap]
rs713066	0.93[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs7470446	0.84[ASN][1000 genomes]
rs750674	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7856924	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7859665	0.81[JPT][hapmap]
rs7869536	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9696167	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762823	chr9:100083872-100105782	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4743077	XPA	cis	parietal	SCAN
rs4743077	VN1R51P	cis	Thyroid	GTEx
rs4743077	RP11-498P14.5	cis	lung	GTEx
rs4743077	RP11-520B13.4	cis	Thyroid	GTEx
rs4743077	TMOD1	cis	cerebellum	SCAN
rs4743077	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs4743077	ANKRD18CP	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100069400-100092800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:100069600-100094400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:100070000-100093800	Weak transcription	Psoas Muscle	Psoas
4	chr9:100070000-100098000	Weak transcription	Small Intestine	intestine
5	chr9:100070000-100100200	Weak transcription	Fetal Heart	heart
6	chr9:100070000-100131400	Weak transcription	Fetal Kidney	kidney
7	chr9:100070200-100092600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr9:100070200-100095000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:100070400-100091800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:100070400-100092800	Weak transcription	Colonic Mucosa	Colon
11	chr9:100070400-100095200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:100071000-100094400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:100071200-100093000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr9:100071600-100093000	Strong transcription	Fetal Stomach	stomach
15	chr9:100071600-100093400	Strong transcription	Brain Anterior Caudate	brain
16	chr9:100071600-100093800	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr9:100071600-100093800	Strong transcription	Ovary	ovary
18	chr9:100071600-100094600	Strong transcription	Brain Angular Gyrus	brain
19	chr9:100071800-100093400	Strong transcription	Adipose Nuclei	Adipose
20	chr9:100071800-100093600	Strong transcription	Left Ventricle	heart
21	chr9:100076000-100093200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:100076000-100093600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:100076200-100092400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:100077000-100106400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
26	chr9:100078000-100091800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr9:100078200-100091800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:100078400-100092800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:100080400-100126400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:100082000-100092000	Strong transcription	Primary T cells from cord blood	blood
31	chr9:100082200-100091600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:100083400-100092600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:100083800-100098400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr9:100083800-100124000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:100084200-100093800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr9:100084400-100093600	Strong transcription	Fetal Muscle Leg	muscle
37	chr9:100084600-100093600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:100085000-100091800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:100085200-100092200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:100085600-100099800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:100085600-100100200	Weak transcription	Primary B cells from cord blood	blood
42	chr9:100086400-100091800	Weak transcription	Esophagus	oesophagus
43	chr9:100086400-100110400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:100086600-100121600	Weak transcription	Right Ventricle	heart
45	chr9:100086600-100132000	Weak transcription	Thymus	Thymus
46	chr9:100086800-100093600	Strong transcription	Aorta	Aorta
47	chr9:100086800-100104000	Weak transcription	Dnd41	blood
48	chr9:100088000-100091800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:100088000-100126200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr9:100088200-100127000	Weak transcription	Duodenum Mucosa	Duodenum

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