Variant report

Variant	rs56375942
Chromosome Location	chr1:174145344-174145345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174145331..174146916-chr1:174149892..174152553,2	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10798307	0.85[EUR][1000 genomes]
rs10912728	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912733	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912735	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912737	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912740	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912741	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912746	0.86[EUR][1000 genomes]
rs10912747	0.86[EUR][1000 genomes]
rs10912750	0.86[EUR][1000 genomes]
rs10912751	0.84[EUR][1000 genomes]
rs10912754	0.85[EUR][1000 genomes]
rs11802158	0.86[EUR][1000 genomes]
rs11807537	0.84[EUR][1000 genomes]
rs12065785	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12074276	0.83[EUR][1000 genomes]
rs12075630	0.92[ASN][1000 genomes]
rs12076453	0.86[EUR][1000 genomes]
rs12076771	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12079214	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079687	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079689	0.86[EUR][1000 genomes]
rs12080977	0.86[EUR][1000 genomes]
rs12081445	0.86[EUR][1000 genomes]
rs12082461	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083540	0.82[EUR][1000 genomes]
rs12085311	0.86[EUR][1000 genomes]
rs12087808	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091155	0.80[EUR][1000 genomes]
rs12091157	0.85[EUR][1000 genomes]
rs12093691	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354141	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407127	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591944	0.81[EUR][1000 genomes]
rs16846717	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846718	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846816	0.86[EUR][1000 genomes]
rs17300775	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350956	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17350991	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17353198	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1934681	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103640	0.86[EUR][1000 genomes]
rs2860907	0.86[EUR][1000 genomes]
rs3086	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233169	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233171	0.80[EUR][1000 genomes]
rs4607949	0.86[EUR][1000 genomes]
rs4650950	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650951	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650958	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650959	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650968	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4650969	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4650981	0.86[EUR][1000 genomes]
rs4652179	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652191	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652193	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652204	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652275	0.85[EUR][1000 genomes]
rs55698100	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56152378	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56158362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239105	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56338048	0.86[EUR][1000 genomes]
rs56404641	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57407575	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59044210	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425277	0.83[EUR][1000 genomes]
rs6656491	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666588	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6668008	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670425	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676161	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678286	0.81[EUR][1000 genomes]
rs6685499	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692437	0.86[EUR][1000 genomes]
rs6694208	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724888	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724889	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711443	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72711448	0.97[ASN][1000 genomes]
rs72711457	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711487	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711492	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711501	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72713503	0.86[EUR][1000 genomes]
rs72713504	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72713505	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs727912	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535987	0.86[EUR][1000 genomes]
rs7551605	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	30 gene(s)	inside rSNPs	diseases
4	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56375942	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs56375942	RP11-160H22.5	cis	Thyroid	GTEx
rs56375942	MRPS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174129600-174164800	Weak transcription	Gastric	stomach
2	chr1:174129600-174173200	Weak transcription	Pancreas	Pancrea
3	chr1:174129800-174145600	Weak transcription	Fetal Thymus	thymus
4	chr1:174129800-174147000	Weak transcription	Fetal Brain Male	brain
5	chr1:174129800-174149600	Weak transcription	Aorta	Aorta
6	chr1:174130000-174157600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:174130200-174145600	Weak transcription	Fetal Stomach	stomach
8	chr1:174130200-174147400	Weak transcription	Hela-S3	cervix
9	chr1:174130800-174156600	Weak transcription	Primary T cells from cord blood	blood
10	chr1:174134800-174159800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:174136200-174150800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:174136400-174160000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:174137800-174155600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:174138400-174160000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:174139000-174159800	Weak transcription	Right Atrium	heart
16	chr1:174139400-174153800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:174141800-174151200	Weak transcription	Fetal Heart	heart
18	chr1:174142000-174146600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:174142000-174153800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:174143400-174148000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:174143600-174145600	ZNF genes & repeats	GM12878-XiMat	blood
22	chr1:174144000-174145600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr1:174144000-174147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:174144000-174147000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:174144000-174151200	Weak transcription	K562	blood
26	chr1:174144000-174151400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:174144000-174178200	Weak transcription	Left Ventricle	heart
28	chr1:174144200-174158000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:174144400-174148200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:174144600-174146000	Weak transcription	Fetal Intestine Small	intestine

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