Variant report

Variant	rs761722
Chromosome Location	chr20:23330842-23330843
allele	C/G
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	CTCF	chr20:23330796-23330974	Lung_OC	lung:	n/a	n/a
2	REST	chr20:23330728-23331186	A549	lung:	n/a	n/a
3	ATF2	chr20:23330387-23331151	GM12878	blood:	n/a	n/a
4	HDAC2	chr20:23330549-23331617	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF143	chr20:23330418-23331523	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr20:23330364-23332519	GM12891	blood:	n/a	n/a
7	CTCF	chr20:23330734-23331008	GM12892	blood:	n/a	n/a
8	TBP	chr20:23330477-23331617	HepG2	liver:	n/a	n/a
9	HCFC1	chr20:23330525-23331989	K562	blood:	n/a	n/a
10	TAF7	chr20:23330840-23331314	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr20:23330592-23332129	HepG2	liver:	n/a	n/a
12	USF1	chr20:23330645-23331546	SK-N-SH	brain:	n/a	chr20:23330993-23331009 chr20:23330982-23330998
13	YY1	chr20:23330629-23331863	A549	lung:	n/a	chr20:23330899-23330913 chr20:23331404-23331418 chr20:23331410-23331419 chr20:23330733-23330742 chr20:23331661-23331675
14	TAF1	chr20:23330571-23332171	ECC-1	luminal epithelium:	n/a	n/a
15	TBP	chr20:23330395-23331585	GM12878	blood:	n/a	n/a
16	E2F6	chr20:23330653-23332176	K562	blood:	n/a	chr20:23331411-23331421 chr20:23331453-23331465 chr20:23331943-23331952 chr20:23330736-23330745
17	MAZ	chr20:23330450-23331607	HepG2	liver:	n/a	chr20:23330889-23330905 chr20:23330889-23330896 chr20:23330744-23330753 chr20:23330734-23330744 chr20:23330887-23330896
18	MAX	chr20:23330337-23332285	Hela-S3	cervix:	n/a	chr20:23331798-23331809 chr20:23330889-23330905 chr20:23331800-23331809 chr20:23331798-23331808 chr20:23330889-23330896 chr20:23331797-23331812 chr20:23330744-23330753 chr20:23330734-23330744 chr20:23330887-23330896 chr20:23331797-23331810 chr20:23331799-23331809
19	POLR2A	chr20:23330296-23332340	HUVEC	blood vessel:	n/a	n/a
20	MAX	chr20:23330413-23332317	NB4	blood:	n/a	chr20:23331798-23331809 chr20:23330889-23330905 chr20:23331800-23331809 chr20:23331798-23331808 chr20:23330889-23330896 chr20:23331797-23331812 chr20:23330744-23330753 chr20:23330734-23330744 chr20:23330887-23330896 chr20:23331797-23331810 chr20:23331799-23331809
21	NFIC	chr20:23330701-23331437	ECC-1	luminal epithelium:	n/a	n/a
22	MYC	chr20:23330725-23331106	GM12878	blood:	n/a	chr20:23330889-23330905 chr20:23330889-23330896 chr20:23330744-23330753 chr20:23330734-23330744 chr20:23330887-23330896
23	POLR2A	chr20:23330384-23331676	HUVEC	blood vessel:	n/a	n/a
24	YY1	chr20:23330602-23331909	GM12878	blood:	n/a	chr20:23330899-23330913 chr20:23331404-23331418 chr20:23331410-23331419 chr20:23330733-23330742 chr20:23331661-23331675
25	POLR2A	chr20:23330365-23331754	Hela-S3	cervix:	n/a	n/a
26	TBL1XR1	chr20:23330463-23331205	K562	blood:	n/a	n/a
27	ZBTB33	chr20:23330717-23331534	A549	lung:	n/a	n/a
28	CTCF	chr20:23330820-23330970	A549	lung:	n/a	n/a
29	GABPA	chr20:23330762-23331954	HepG2	liver:	n/a	chr20:23331062-23331071
30	SIN3AK20	chr20:23330803-23331621	HepG2	liver:	n/a	n/a
31	POLR2A	chr20:23330622-23332092	Gliobla	brain:	n/a	n/a
32	POLR2A	chr20:23330464-23331627	HepG2	liver:	n/a	n/a
33	MTA3	chr20:23330335-23332333	GM12878	blood:	n/a	n/a
34	PML	chr20:23330519-23331590	GM12878	blood:	n/a	n/a
35	GABPA	chr20:23330603-23331999	K562	blood:	n/a	chr20:23331062-23331071
36	GABPA	chr20:23330642-23332267	A549	lung:	n/a	chr20:23331062-23331071
37	ELF1	chr20:23330451-23332103	MCF-7	breast:	n/a	chr20:23331411-23331423 chr20:23331305-23331314 chr20:23330645-23330658 chr20:23331487-23331499
38	JUND	chr20:23330516-23331992	A549	lung:	n/a	chr20:23330737-23330746
39	ETS1	chr20:23330527-23331575	A549	lung:	n/a	chr20:23330733-23330744 chr20:23330808-23330823 chr20:23330739-23330750 chr20:23331352-23331361
40	CTCF	chr20:23330807-23330970	MCF-7	breast:	n/a	n/a
41	POLR2A	chr20:23330302-23332250	ECC-1	luminal epithelium:	n/a	n/a
42	BACH1	chr20:23330305-23332189	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr20:23330594-23332195	MCF-7	breast:	n/a	n/a
44	MEF2A	chr20:23330678-23331534	GM12878	blood:	n/a	n/a
45	POLR2A	chr20:23329986-23332360	Raji	blood:	n/a	n/a
46	POLR2A	chr20:23330598-23332181	MCF-7	breast:	n/a	n/a
47	POLR2A	chr20:23330408-23331574	HCT-116	colon:	n/a	n/a
48	TEAD4	chr20:23330491-23331652	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr20:23330470-23332390	HepG2	liver:	n/a	n/a
50	ELF1	chr20:23330362-23331706	MCF-7	breast:	n/a	chr20:23331411-23331423 chr20:23331305-23331314 chr20:23330645-23330658 chr20:23331487-23331499

No.	Distal block	Cell Line	Cell type
1	chr20:23330412..23330928-chr20:23426987..23427635,2	MCF-7	breast:
2	chr20:23330561..23331162-chr3:137906148..137906729,2	Hela-S3	cervix:
3	chr20:23187473..23190139-chr20:23328538..23331366,2	MCF-7	breast:
4	chr12:122502015..122502839-chr20:23330558..23331073,2	NB4	blood:
5	chr20:23330052..23330922-chr20:23586934..23587533,2	MCF-7	breast:
6	chr2:179541157..179541657-chr20:23330512..23331015,2	Hela-S3	cervix:
7	chr20:23328647..23330996-chr20:23399236..23401652,2	K562	blood:
8	chr10:6244548..6245207-chr20:23330568..23331191,2	HCT-116	colon:
9	chr20:23321273..23323325-chr20:23328933..23330875,2	K562	blood:
10	chr20:23022684..23024263-chr20:23328966..23331361,2	MCF-7	breast:
11	chr20:23112159..23115128-chr20:23328465..23330957,2	K562	blood:
12	chr20:23029084..23031719-chr20:23329992..23332006,2	K562	blood:

Variant related genes	Relation type
NXT1	TF binding region
ENSG00000233746	Chromatin interaction
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction
ENSG00000256546	Chromatin interaction
ENSG00000178726	Chromatin interaction
ENSG00000114098	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1076776	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12625164	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17757228	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17757442	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17830281	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1936011	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277765	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2281428	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2281434	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2295238	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34648279	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3736755	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3746733	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3746737	0.86[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3761274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3761275	0.87[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3827085	0.87[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827086	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55851398	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56094936	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs56334525	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132600	0.86[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132605	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6132606	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132609	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6132610	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6132617	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137901	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6137907	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137910	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137913	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137914	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137915	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137917	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137919	0.85[CEU][hapmap];0.94[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6137920	0.85[CEU][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6137927	0.86[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137929	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137930	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137931	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137936	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137937	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137938	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137939	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137941	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6137945	0.86[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137947	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137948	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137950	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6137951	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8183135	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs761722	NXT1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23329800-23331200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr20:23329800-23331200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr20:23329800-23333600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:23330000-23331000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr20:23330000-23331000	Flanking Bivalent TSS/Enh	HepG2	liver
6	chr20:23330000-23331600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr20:23330000-23331800	Active TSS	Duodenum Mucosa	Duodenum
8	chr20:23330000-23331800	Active TSS	Fetal Muscle Trunk	muscle
9	chr20:23330000-23332000	Active TSS	Rectal Smooth Muscle	rectum
10	chr20:23330000-23332000	Active TSS	Right Atrium	heart
11	chr20:23330000-23332400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr20:23330000-23332600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr20:23330000-23332600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr20:23330000-23332800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:23330200-23331000	Flanking Active TSS	Fetal Muscle Leg	muscle
16	chr20:23330200-23331200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr20:23330200-23331200	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr20:23330200-23331600	Active TSS	Colonic Mucosa	Colon
19	chr20:23330200-23331800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr20:23330200-23331800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr20:23330200-23331800	Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr20:23330200-23331800	Active TSS	Stomach Smooth Muscle	stomach
23	chr20:23330200-23332200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr20:23330200-23332200	Active TSS	Aorta	Aorta
25	chr20:23330200-23332200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr20:23330200-23332200	Active TSS	Fetal Intestine Large	intestine
27	chr20:23330200-23332200	Active TSS	Fetal Intestine Small	intestine
28	chr20:23330200-23332200	Active TSS	Fetal Kidney	kidney
29	chr20:23330200-23332200	Active TSS	Right Ventricle	heart
30	chr20:23330200-23332200	Active TSS	Small Intestine	intestine
31	chr20:23330200-23332200	Active TSS	NHLF	lung
32	chr20:23330200-23332400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:23330200-23332400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr20:23330200-23332400	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr20:23330200-23332400	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr20:23330200-23332400	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr20:23330200-23332400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr20:23330200-23332400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr20:23330200-23332400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr20:23330200-23332400	Active TSS	Psoas Muscle	Psoas
41	chr20:23330200-23332400	Active TSS	HMEC	breast
42	chr20:23330200-23332400	Active TSS	HSMM	muscle
43	chr20:23330200-23332400	Active TSS	HSMMtube	muscle
44	chr20:23330200-23332600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr20:23330200-23332600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr20:23330200-23332600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr20:23330200-23332600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr20:23330200-23332600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr20:23330200-23332600	Active TSS	A549	lung
50	chr20:23330200-23332600	Active TSS	Hela-S3	cervix

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