Variant report

Variant	rs73234873
Chromosome Location	chr7:127292004-127292005
allele	C/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	SP1	chr7:127291834-127292310	GM12878	blood:	n/a	chr7:127292111-127292123 chr7:127292128-127292149 chr7:127292113-127292122 chr7:127291923-127291934
2	POLR2A	chr7:127291013-127292731	HUVEC	blood vessel:	n/a	n/a
3	MAX	chr7:127291253-127292640	SK-N-SH	brain:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
4	GATA2	chr7:127291749-127292758	SH-SY5Y	brain:	n/a	n/a
5	MYC	chr7:127291004-127293350	K562	blood:	n/a	chr7:127293151-127293161 chr7:127291654-127291663 chr7:127292615-127292625
6	E2F6	chr7:127291305-127292704	H1-hESC	embryonic stem cell:	n/a	chr7:127291641-127291655
7	YY1	chr7:127291473-127292706	SK-N-SH_RA	brain:	n/a	chr7:127292228-127292237 chr7:127292179-127292193 chr7:127292229-127292240
8	TAF1	chr7:127291488-127292798	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr7:127291214-127292747	NB4	blood:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
10	E2F6	chr7:127291334-127292593	K562	blood:	n/a	chr7:127291641-127291655
11	REST	chr7:127291575-127292563	HepG2	liver:	n/a	chr7:127292179-127292192
12	RFX5	chr7:127291676-127292414	GM12878	blood:	n/a	n/a
13	TCF3	chr7:127291668-127292021	GM12878	blood:	n/a	n/a
14	ZMIZ1	chr7:127291131-127292885	K562	blood:	n/a	n/a
15	TCF7L2	chr7:127291876-127292030	PANC-1	pancreas:	n/a	n/a
16	ZNF143	chr7:127291747-127292594	Hela-S3	cervix:	n/a	chr7:127292566-127292584
17	MYC	chr7:127291168-127293291	K562	blood:	n/a	chr7:127293151-127293161 chr7:127291654-127291663 chr7:127292615-127292625
18	CEBPB	chr7:127291711-127292463	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr7:127291188-127292540	K562	blood:	n/a	n/a
20	POLR2A	chr7:127290908-127292823	K562	blood:	n/a	n/a
21	YY1	chr7:127291571-127292720	ECC-1	luminal epithelium:	n/a	chr7:127292228-127292237 chr7:127292179-127292193 chr7:127292229-127292240
22	MAFK	chr7:127291275-127292511	K562	blood:	n/a	n/a
23	POLR2A	chr7:127291231-127293124	K562	blood:	n/a	n/a
24	SP2	chr7:127291869-127292351	H1-hESC	embryonic stem cell:	n/a	chr7:127292107-127292122 chr7:127292137-127292147
25	TAF1	chr7:127291696-127292466	GM12891	blood:	n/a	n/a
26	MTA3	chr7:127290837-127293079	GM12878	blood:	n/a	n/a
27	EBF1	chr7:127291644-127292098	GM12878	blood:	n/a	chr7:127291929-127291940
28	E2F6	chr7:127291053-127292983	K562	blood:	n/a	chr7:127291641-127291655
29	HEY1	chr7:127291193-127292089	K562	blood:	n/a	n/a
30	POLR2A	chr7:127291396-127292646	GM12878	blood:	n/a	n/a
31	MAX	chr7:127291422-127293295	Hela-S3	cervix:	n/a	chr7:127293151-127293161 chr7:127291654-127291663 chr7:127292615-127292625
32	CREB1	chr7:127291280-127292832	H1-hESC	embryonic stem cell:	n/a	n/a
33	CHD1	chr7:127291202-127293127	GM12878	blood:	n/a	n/a
34	MYC	chr7:127291280-127293360	K562	blood:	n/a	chr7:127293151-127293161 chr7:127291654-127291663 chr7:127292615-127292625
35	SIN3AK20	chr7:127291733-127292498	HepG2	liver:	n/a	n/a
36	GABPA	chr7:127291602-127292508	K562	blood:	n/a	chr7:127292203-127292212 chr7:127292201-127292215
37	MAX	chr7:127291318-127292690	HepG2	liver:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
38	USF2	chr7:127291805-127292005	HepG2	liver:	n/a	n/a
39	POLR2A	chr7:127291230-127292753	K562	blood:	n/a	n/a
40	SRF	chr7:127291859-127292211	HepG2	liver:	n/a	n/a
41	MYC	chr7:127291387-127292661	K562	blood:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
42	EP300	chr7:127291596-127292136	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr7:127291102-127292793	PFSK-1	brain:	n/a	n/a
44	E2F1	chr7:127291589-127292422	Hela-S3	cervix:	n/a	chr7:127291641-127291655
45	ATF2	chr7:127291324-127292509	H1-hESC	embryonic stem cell:	n/a	chr7:127291969-127291983
46	TAF1	chr7:127291530-127292618	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr7:127291325-127292607	A549	lung:	n/a	n/a
48	POU2F2	chr7:127291949-127292563	GM12891	blood:	n/a	n/a
49	POLR2A	chr7:127291000-127292910	GM19099	blood:	n/a	n/a
50	YY1	chr7:127291314-127292623	K562	blood:	n/a	chr7:127292228-127292237 chr7:127292179-127292193 chr7:127292229-127292240

No.	Distal block	Cell Line	Cell type
1	chr7:127222868..127230871-chr7:127290370..127294912,16	K562	blood:
2	chr7:127031057..127033330-chr7:127290561..127293507,3	MCF-7	breast:
3	chr13:46038900..46039511-chr7:127291480..127292315,2	Hela-S3	cervix:
4	chr7:127224289..127226040-chr7:127290840..127293019,2	MCF-7	breast:
5	chr2:54683448..54684022-chr7:127291404..127292021,2	HCT-116	colon:
6	chr7:127291173..127294029-chr7:127587944..127590935,2	MCF-7	breast:
7	chr7:127223375..127232960-chr7:127286940..127295803,24	K562	blood:
8	chr7:127029920..127034279-chr7:127291168..127294285,4	MCF-7	breast:
9	chr7:127029926..127034103-chr7:127290516..127296284,10	K562	blood:
10	chr7:127290259..127292033-chr7:127774841..127777045,2	K562	blood:
11	chr7:127226125..127229974-chr7:127289784..127293571,8	MCF-7	breast:
12	chr12:6601976..6602701-chr7:127291308..127292165,2	Hela-S3	cervix:
13	chr7:127028627..127034604-chr7:127290902..127294330,10	K562	blood:
14	chr5:68664784..68665553-chr7:127291574..127292566,2	NB4	blood:
15	chr1:16840307..16840955-chr7:127291583..127292147,2	Hela-S3	cervix:
16	chr7:127232880..127234701-chr7:127291672..127293969,3	K562	blood:
17	chr1:212781981..212782558-chr7:127291551..127292258,2	Hela-S3	cervix:
18	chr7:127232149..127233978-chr7:127290816..127293700,2	MCF-7	breast:
19	chr7:127226810..127231119-chr7:127290066..127293801,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAX4-1	chr7:127291727-127292066	XLOC_006596

Variant related genes	Relation type
SND1	TF binding region
ENSG00000048405	Chromatin interaction
ENSG00000010292	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000106328	Chromatin interaction
ENSG00000136152	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000111639	Chromatin interaction
ENSG00000179562	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000197157	Chromatin interaction
ENSG00000004059	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12375023	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12531847	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12540357	0.85[EUR][1000 genomes]
rs12706816	0.87[EUR][1000 genomes]
rs12706818	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12706819	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12706820	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12706821	0.86[EUR][1000 genomes]
rs12706822	0.85[EUR][1000 genomes]
rs13221709	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13229973	0.86[EUR][1000 genomes]
rs13231367	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13236338	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13238924	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13246200	0.85[EUR][1000 genomes]
rs13246286	0.86[EUR][1000 genomes]
rs1348103	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1419970	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1468701	0.85[EUR][1000 genomes]
rs17151466	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17151488	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17151507	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34026100	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34839191	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35154268	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35660964	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58406876	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67632185	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67827668	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6959487	0.93[EUR][1000 genomes]
rs73234874	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7458839	0.85[EUR][1000 genomes]
rs7809182	0.85[EUR][1000 genomes]
rs7810024	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs894062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9649027	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1031658	chr7:127266882-127376775	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73234873	SND1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127290800-127292600	Active TSS	Primary T cells from cord blood	blood
2	chr7:127290800-127294000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:127290800-127294000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr7:127291000-127292600	Active TSS	Brain Anterior Caudate	brain
5	chr7:127291000-127292600	Active TSS	Brain Germinal Matrix	brain
6	chr7:127291000-127292600	Active TSS	Brain Substantia Nigra	brain
7	chr7:127291000-127292600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr7:127291000-127292800	Active TSS	Colon Smooth Muscle	Colon
9	chr7:127291000-127293000	Active TSS	Liver	Liver
10	chr7:127291000-127293000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:127291000-127293000	Active TSS	Stomach Smooth Muscle	stomach
12	chr7:127291000-127293200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:127291000-127293200	Active TSS	A549	lung
14	chr7:127291000-127293400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:127291000-127293400	Active TSS	Psoas Muscle	Psoas
16	chr7:127291000-127293600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:127291000-127293800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr7:127291000-127293800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:127291000-127293800	Active TSS	HSMM	muscle
20	chr7:127291000-127294200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr7:127291200-127292200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:127291200-127292600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr7:127291200-127292600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr7:127291200-127292600	Active TSS	Brain Angular Gyrus	brain
25	chr7:127291200-127292600	Active TSS	Brain Cingulate Gyrus	brain
26	chr7:127291200-127293000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr7:127291200-127293000	Active TSS	Esophagus	oesophagus
28	chr7:127291200-127293200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:127291200-127293200	Active TSS	Aorta	Aorta
30	chr7:127291200-127293200	Active TSS	Left Ventricle	heart
31	chr7:127291200-127293400	Active TSS	H9 Cell Line	embryonic stem cell
32	chr7:127291200-127293400	Active TSS	Colonic Mucosa	Colon
33	chr7:127291200-127293400	Active TSS	NHDF-Ad	bronchial
34	chr7:127291200-127293600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:127291200-127293800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:127291200-127294000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:127291200-127294400	Active TSS	Pancreas	Pancrea
38	chr7:127291200-127294600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:127291200-127294600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr7:127291400-127292200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:127291400-127292400	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr7:127291400-127292600	Active TSS	Rectal Smooth Muscle	rectum
43	chr7:127291400-127292600	Active TSS	Spleen	Spleen
44	chr7:127291400-127292800	Active TSS	Fetal Intestine Small	intestine
45	chr7:127291400-127292800	Active TSS	Thymus	Thymus
46	chr7:127291400-127293000	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr7:127291400-127293000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:127291400-127293000	Active TSS	Duodenum Mucosa	Duodenum
49	chr7:127291400-127293000	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr7:127291400-127293200	Active TSS	Gastric	stomach

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