Variant report

Variant	rs3107873
Chromosome Location	chr7:66654740-66654741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10081276	0.86[EUR][1000 genomes]
rs10081302	0.85[EUR][1000 genomes]
rs10081331	0.86[EUR][1000 genomes]
rs10081333	0.86[EUR][1000 genomes]
rs10081344	0.86[EUR][1000 genomes]
rs10230059	0.83[EUR][1000 genomes]
rs10232876	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10233388	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10233507	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10243421	0.85[EUR][1000 genomes]
rs10247272	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10254788	0.85[EUR][1000 genomes]
rs10258678	0.83[EUR][1000 genomes]
rs10272347	0.80[EUR][1000 genomes]
rs10272424	0.80[EUR][1000 genomes]
rs10272591	0.80[EUR][1000 genomes]
rs10273692	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10277509	0.89[EUR][1000 genomes]
rs10950062	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10950064	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11760347	0.82[EUR][1000 genomes]
rs11761100	0.82[EUR][1000 genomes]
rs11761577	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11764376	0.81[EUR][1000 genomes]
rs11772455	0.82[EUR][1000 genomes]
rs11773274	0.82[EUR][1000 genomes]
rs11773730	0.83[EUR][1000 genomes]
rs11976638	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12154257	0.81[EUR][1000 genomes]
rs12154688	0.83[EUR][1000 genomes]
rs12155330	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13244997	0.86[EUR][1000 genomes]
rs1581502	0.83[EUR][1000 genomes]
rs17139656	0.83[EUR][1000 genomes]
rs1815101	0.83[EUR][1000 genomes]
rs2019826	0.84[EUR][1000 genomes]
rs2421393	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2421398	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421404	0.87[EUR][1000 genomes]
rs2421405	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2421425	0.81[EUR][1000 genomes]
rs28497071	0.83[EUR][1000 genomes]
rs28556313	0.83[EUR][1000 genomes]
rs28749249	0.80[EUR][1000 genomes]
rs28750410	0.80[EUR][1000 genomes]
rs28767482	0.80[EUR][1000 genomes]
rs28806258	0.85[EUR][1000 genomes]
rs28808071	0.86[EUR][1000 genomes]
rs28860910	0.86[EUR][1000 genomes]
rs2901424	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2949096	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2949109	0.84[EUR][1000 genomes]
rs34145691	0.80[EUR][1000 genomes]
rs34146912	0.82[EUR][1000 genomes]
rs34176733	0.86[EUR][1000 genomes]
rs34463275	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34566330	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34567129	0.87[EUR][1000 genomes]
rs34574768	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs34654147	0.80[EUR][1000 genomes]
rs35064061	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35120837	0.85[EUR][1000 genomes]
rs35290283	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35336066	0.89[EUR][1000 genomes]
rs35387955	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35399585	0.82[EUR][1000 genomes]
rs35521959	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35599428	0.83[EUR][1000 genomes]
rs35649461	0.82[EUR][1000 genomes]
rs35669114	0.82[EUR][1000 genomes]
rs35723315	0.81[EUR][1000 genomes]
rs35918453	0.86[EUR][1000 genomes]
rs35970624	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35982871	0.81[EUR][1000 genomes]
rs3897072	0.84[EUR][1000 genomes]
rs3980775	0.86[EUR][1000 genomes]
rs3980790	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4103731	0.84[EUR][1000 genomes]
rs4145350	0.80[EUR][1000 genomes]
rs4295533	0.80[EUR][1000 genomes]
rs4383874	0.83[EUR][1000 genomes]
rs4433024	0.85[EUR][1000 genomes]
rs4486076	0.82[EUR][1000 genomes]
rs4496851	0.82[EUR][1000 genomes]
rs4504527	0.83[EUR][1000 genomes]
rs4524666	0.83[EUR][1000 genomes]
rs4535609	0.83[EUR][1000 genomes]
rs4636084	0.82[EUR][1000 genomes]
rs4717354	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4718475	0.86[EUR][1000 genomes]
rs4718477	0.86[EUR][1000 genomes]
rs4718478	0.83[EUR][1000 genomes]
rs55756354	0.80[EUR][1000 genomes]
rs55921608	0.82[EUR][1000 genomes]
rs56001319	0.86[EUR][1000 genomes]
rs61061833	0.85[EUR][1000 genomes]
rs6460333	0.83[EUR][1000 genomes]
rs66806481	0.83[EUR][1000 genomes]
rs66954241	0.83[EUR][1000 genomes]
rs67650940	0.82[EUR][1000 genomes]
rs67855845	0.80[EUR][1000 genomes]
rs67890875	0.82[EUR][1000 genomes]
rs6942913	0.82[EUR][1000 genomes]
rs6943439	0.82[EUR][1000 genomes]
rs6944637	0.81[EUR][1000 genomes]
rs6944968	0.81[EUR][1000 genomes]
rs6947488	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6947514	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6948588	0.82[EUR][1000 genomes]
rs6948793	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6949429	0.86[EUR][1000 genomes]
rs6951468	0.83[EUR][1000 genomes]
rs6954515	0.82[EUR][1000 genomes]
rs6954642	0.82[EUR][1000 genomes]
rs6961084	0.82[EUR][1000 genomes]
rs6963793	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6964179	0.84[EUR][1000 genomes]
rs6967381	0.86[EUR][1000 genomes]
rs6967876	0.86[EUR][1000 genomes]
rs6979001	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73140602	0.80[EUR][1000 genomes]
rs73142604	0.80[EUR][1000 genomes]
rs73142680	0.82[EUR][1000 genomes]
rs73377106	0.81[EUR][1000 genomes]
rs7779069	0.83[EUR][1000 genomes]
rs7792907	0.83[EUR][1000 genomes]
rs7811233	0.81[EUR][1000 genomes]
rs9654771	0.80[EUR][1000 genomes]
rs9769387	0.82[EUR][1000 genomes]
rs9886204	0.85[EUR][1000 genomes]
rs9886206	0.85[EUR][1000 genomes]
rs9886263	0.86[EUR][1000 genomes]
rs9886290	0.85[EUR][1000 genomes]
rs9886306	0.85[EUR][1000 genomes]
rs9886326	0.85[EUR][1000 genomes]
rs9986784	0.84[EUR][1000 genomes]
rs9986995	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases
5	esv2422035	chr7:66621964-66676630	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1032237	chr7:66644492-66785029	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv970518	chr7:66647675-66742783	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3107873	TYW1	cis	Esophagus Mucosa	GTEx
rs3107873	TYW1	cis	Muscle Skeletal	GTEx
rs3107873	TYW1	cis	Heart Left Ventricle	GTEx
rs3107873	TYW1	Cis_1M	lymphoblastoid	RTeQTL
rs3107873	TYW1	cis	Nerve Tibial	GTEx
rs3107873	GS1-124K5.4	cis	Nerve Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66621600-66672000	Weak transcription	Fetal Intestine Large	intestine
2	chr7:66628600-66684600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:66640600-66677200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr7:66643000-66660000	Weak transcription	Dnd41	blood
5	chr7:66644400-66659400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:66644400-66683000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:66644600-66659400	Weak transcription	Fetal Intestine Small	intestine
8	chr7:66644800-66660200	Weak transcription	Adipose Nuclei	Adipose
9	chr7:66645000-66657600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:66645000-66660000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:66645800-66655600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:66645800-66660000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:66647000-66677400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:66647600-66657800	Weak transcription	Right Atrium	heart
15	chr7:66647600-66661400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:66647800-66659800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr7:66647800-66660000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:66648200-66679800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:66648800-66667200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:66649000-66658200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:66649200-66677200	Weak transcription	Right Ventricle	heart
22	chr7:66649200-66679200	Weak transcription	NHEK	skin
23	chr7:66650000-66660000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:66650200-66657800	Weak transcription	Ovary	ovary
25	chr7:66650600-66655400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:66650600-66655800	Weak transcription	Fetal Thymus	thymus
27	chr7:66650600-66661800	Weak transcription	Fetal Stomach	stomach
28	chr7:66650800-66654800	Weak transcription	HSMM	muscle
29	chr7:66651200-66675400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr7:66651800-66657600	Weak transcription	GM12878-XiMat	blood
31	chr7:66652800-66675600	Weak transcription	Aorta	Aorta
32	chr7:66653400-66655200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:66653400-66655600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:66653800-66656200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr7:66654000-66656200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr7:66654000-66656400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr7:66654000-66656400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr7:66654000-66656600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr7:66654200-66655000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr7:66654200-66655200	Enhancers	Psoas Muscle	Psoas
41	chr7:66654200-66655400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:66654200-66656400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr7:66654200-66656400	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr7:66654200-66656400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr7:66654200-66656400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr7:66654200-66656600	Enhancers	K562	blood
47	chr7:66654200-66658000	Enhancers	HSMMtube	muscle
48	chr7:66654200-66658200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr7:66654400-66656000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr7:66654400-66657600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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