Variant report

Variant	rs1591944
Chromosome Location	chr1:174174055-174174056
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ETS1	chr1:174173715-174174199	GM12878	blood:	n/a	n/a
2	RUNX3	chr1:174173740-174174509	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr1:174173781-174174416	K562	blood:	n/a	n/a
4	USF1	chr1:174173841-174174438	HCT-116	colon:	n/a	chr1:174174193-174174204
5	CUX1	chr1:174173863-174174412	K562	blood:	n/a	n/a
6	POLR2A	chr1:174173679-174174296	GM12892	blood:	n/a	n/a
7	FOXM1	chr1:174173734-174174485	GM12878	blood:	n/a	n/a
8	NFATC1	chr1:174173604-174174681	GM12878	blood:	n/a	n/a
9	ZBTB33	chr1:174173671-174174184	K562	blood:	n/a	n/a
10	MEF2A	chr1:174173795-174174441	GM12878	blood:	n/a	n/a
11	ELF1	chr1:174173762-174174415	GM12878	blood:	n/a	n/a
12	IRF1	chr1:174173939-174174324	K562	blood:	n/a	n/a
13	ZBTB33	chr1:174173689-174174094	GM12878	blood:	n/a	n/a
14	KAP1	chr1:174173788-174174406	HEK293	kidney:	n/a	n/a
15	POLR2A	chr1:174173730-174174291	GM12878	blood:	n/a	n/a
16	ZBTB33	chr1:174173693-174174199	K562	blood:	n/a	n/a
17	MTA3	chr1:174173649-174174505	GM12878	blood:	n/a	n/a
18	IRF4	chr1:174173749-174174130	GM12878	blood:	n/a	n/a
19	EP300	chr1:174173371-174174367	K562	blood:	n/a	n/a
20	FOSL2	chr1:174173964-174174467	HepG2	liver:	n/a	chr1:174174227-174174238
21	POLR2A	chr1:174173719-174174393	GM12892	blood:	n/a	n/a
22	TAF1	chr1:174173780-174174133	GM12891	blood:	n/a	n/a
23	ZBTB33	chr1:174173680-174174174	GM12878	blood:	n/a	n/a
24	MAX	chr1:174173743-174174404	K562	blood:	n/a	chr1:174174193-174174203
25	NFIC	chr1:174173618-174174557	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:174173690-174174250	GM12878	blood:	n/a	n/a
27	CBX3	chr1:174173680-174174550	HCT-116	colon:	n/a	n/a
28	MAX	chr1:174173767-174174524	HCT-116	colon:	n/a	chr1:174174193-174174203
29	CBX3	chr1:174173498-174174413	K562	blood:	n/a	n/a
30	POLR2A	chr1:174173877-174174125	K562	blood:	n/a	n/a
31	POLR2A	chr1:174173828-174174144	GM12878	blood:	n/a	n/a
32	MAFF	chr1:174173937-174174358	K562	blood:	n/a	n/a
33	JUND	chr1:174173339-174174788	K562	blood:	n/a	chr1:174174228-174174239
34	RUNX3	chr1:174173721-174174493	GM12878	blood:	n/a	n/a
35	YY1	chr1:174173840-174174155	K562	blood:	n/a	n/a
36	E2F6	chr1:174173840-174174121	K562	blood:	n/a	n/a
37	POLR2A	chr1:174173670-174174399	GM12892	blood:	n/a	n/a
38	ATF1	chr1:174173860-174174306	K562	blood:	n/a	n/a
39	USF1	chr1:174173758-174174419	K562	blood:	n/a	chr1:174174193-174174204
40	TAF1	chr1:174173846-174174121	K562	blood:	n/a	n/a
41	JUND	chr1:174174045-174174408	Hela-S3	cervix:	n/a	chr1:174174228-174174239
42	YY1	chr1:174173863-174174110	GM12878	blood:	n/a	n/a
43	FOSL1	chr1:174173950-174174438	HCT-116	colon:	n/a	n/a
44	MAX	chr1:174173797-174174362	K562	blood:	n/a	chr1:174174193-174174203
45	TBP	chr1:174173876-174174119	K562	blood:	n/a	n/a
46	USF1	chr1:174173891-174174387	K562	blood:	n/a	chr1:174174193-174174204
47	HEY1	chr1:174173757-174174170	K562	blood:	n/a	n/a
48	CBX3	chr1:174173657-174174432	K562	blood:	n/a	n/a
49	POLR2A	chr1:174173786-174174099	GM12878	blood:	n/a	n/a
50	ZBTB33	chr1:174173767-174174124	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:174126473..174129407-chr1:174172803..174176660,7	K562	blood:
2	chr1:174169989..174171765-chr1:174171980..174175775,3	K562	blood:
3	chr1:174159869..174162419-chr1:174173364..174176167,2	K562	blood:

Variant related genes	Relation type
ENSG00000238872	TF binding region
ENSG00000227373	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10798307	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10798309	0.82[AFR][1000 genomes]
rs10912733	0.80[AFR][1000 genomes]
rs10912735	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10912737	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10912740	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10912741	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10912746	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10912747	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10912750	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10912751	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10912753	0.82[AFR][1000 genomes]
rs10912754	0.93[EUR][1000 genomes]
rs10912757	0.90[AFR][1000 genomes]
rs10912762	0.90[AFR][1000 genomes]
rs11802158	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11807537	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12059434	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12065785	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12074276	0.90[EUR][1000 genomes]
rs12076453	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12076771	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12079214	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12079687	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12079689	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12080977	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12081445	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12082461	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12083540	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12085311	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12087808	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12091012	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12091155	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12091157	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12093691	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12097252	0.90[AFR][1000 genomes]
rs12354141	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1417186	0.81[EUR][1000 genomes]
rs16846717	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16846718	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16846816	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17300775	0.81[EUR][1000 genomes]
rs1934681	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2103640	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2860907	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3086	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4233169	0.80[AFR][1000 genomes]
rs4233171	0.88[EUR][1000 genomes]
rs4607949	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4650950	0.81[AFR][1000 genomes]
rs4650951	0.81[AFR][1000 genomes]
rs4650958	0.82[EUR][1000 genomes]
rs4650959	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4650968	0.93[EUR][1000 genomes]
rs4650969	0.93[EUR][1000 genomes]
rs4650981	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4652191	0.82[AFR][1000 genomes]
rs4652193	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4652275	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55698100	0.92[EUR][1000 genomes]
rs56158362	0.81[EUR][1000 genomes]
rs56239105	0.81[EUR][1000 genomes]
rs56338048	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56375942	0.81[EUR][1000 genomes]
rs56404641	0.81[EUR][1000 genomes]
rs59649440	0.86[EUR][1000 genomes]
rs6425277	0.90[EUR][1000 genomes]
rs6666588	0.93[EUR][1000 genomes]
rs6670425	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6676161	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6678209	0.88[AFR][1000 genomes]
rs6678286	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6685499	0.88[AFR][1000 genomes]
rs6692437	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6693198	0.88[AFR][1000 genomes]
rs724888	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs724889	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72711487	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72711501	0.91[EUR][1000 genomes]
rs72713503	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72713504	0.93[EUR][1000 genomes]
rs72713505	0.93[EUR][1000 genomes]
rs727912	0.82[AFR][1000 genomes]
rs7535987	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7551605	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1591944	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs1591944	RABGAP1L	cis	Esophagus Muscularis	GTEx
rs1591944	RP11-160H22.5	cis	Thyroid	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174144000-174178200	Weak transcription	Left Ventricle	heart
2	chr1:174160800-174186600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:174161000-174176200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:174161200-174176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:174161600-174175000	Weak transcription	NHDF-Ad	bronchial
6	chr1:174161600-174178600	Weak transcription	Primary B cells from cord blood	blood
7	chr1:174162000-174189600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:174163800-174178200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:174167200-174178400	Weak transcription	Fetal Stomach	stomach
10	chr1:174167400-174175000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:174170800-174178000	Weak transcription	Fetal Intestine Small	intestine
12	chr1:174172200-174179800	ZNF genes & repeats	GM12878-XiMat	blood
13	chr1:174172600-174175600	Weak transcription	Primary T cells from cord blood	blood
14	chr1:174172800-174174400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr1:174172800-174175600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:174172800-174190600	Weak transcription	Fetal Intestine Large	intestine
17	chr1:174172800-174191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:174173000-174174600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:174173000-174176400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:174173200-174175200	Enhancers	HepG2	liver
21	chr1:174173200-174191400	Weak transcription	Brain Anterior Caudate	brain
22	chr1:174173400-174175800	Enhancers	Fetal Heart	heart
23	chr1:174173400-174176000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:174173400-174176000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr1:174173400-174176000	Flanking Active TSS	K562	blood
26	chr1:174173600-174174600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:174173600-174175400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:174173600-174176000	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:174173600-174176000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:174173600-174176200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:174173600-174176800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr1:174173800-174174200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:174173800-174174200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:174173800-174174200	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr1:174173800-174174400	Enhancers	Psoas Muscle	Psoas
36	chr1:174173800-174174400	Enhancers	Dnd41	blood
37	chr1:174173800-174174600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr1:174173800-174174600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr1:174173800-174175600	Enhancers	Hela-S3	cervix
40	chr1:174174000-174174200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:174174000-174174400	Enhancers	Stomach Mucosa	stomach
42	chr1:174174000-174186200	Weak transcription	Ovary	ovary

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