Variant report

Variant	rs58406876
Chromosome Location	chr7:127353843-127353844
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	POLR2A	chr7:127353784-127354081	K562	blood:	n/a	n/a
2	POLR2A	chr7:127353504-127354099	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127346393..127350430-chr7:127351346..127355414,4	K562	blood:
2	chr7:127342621..127344330-chr7:127352147..127354125,2	K562	blood:

Variant related genes	Relation type
SND1	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10487499	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487502	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154492	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375023	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532894	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540357	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706816	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12706820	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706821	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706823	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221709	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227201	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348103	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.90[EUR][1000 genomes]
rs17151466	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151507	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17676654	1.00[ASN][1000 genomes]
rs327508	1.00[ASN][1000 genomes]
rs34026100	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34839191	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154268	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35660964	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660321	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67632185	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959487	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232968	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234873	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73234874	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741094	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7458839	0.91[EUR][1000 genomes]
rs7785596	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	0.91[EUR][1000 genomes]
rs7810024	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894062	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649027	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649512	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	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
7	nsv1030387	chr7:127348973-127455890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58406876	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	chr7:127324800-127372200	Weak transcription	Fetal Heart	heart
2	chr7:127325600-127363000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:127326000-127354400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:127326000-127355600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr7:127326400-127356600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr7:127326600-127355200	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:127326600-127379800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr7:127326800-127371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:127327000-127355200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr7:127330000-127355600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:127331600-127375600	Strong transcription	Fetal Thymus	thymus
12	chr7:127333800-127354200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:127334400-127376600	Weak transcription	Fetal Brain Male	brain
14	chr7:127334600-127354400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:127335000-127359400	Strong transcription	Hela-S3	cervix
16	chr7:127339000-127357400	Weak transcription	Small Intestine	intestine
17	chr7:127339400-127371000	Weak transcription	Right Atrium	heart
18	chr7:127344600-127371200	Weak transcription	Brain Germinal Matrix	brain
19	chr7:127345000-127362000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr7:127345200-127357400	Weak transcription	Spleen	Spleen
21	chr7:127345400-127361000	Weak transcription	Colonic Mucosa	Colon
22	chr7:127347800-127365200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr7:127347800-127383000	Strong transcription	NHEK	skin
24	chr7:127348600-127357800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr7:127349000-127360400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr7:127349200-127356000	Strong transcription	Osteobl	bone
27	chr7:127349400-127357400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:127349400-127357400	Weak transcription	Brain Anterior Caudate	brain
29	chr7:127349400-127357400	Weak transcription	Esophagus	oesophagus
30	chr7:127349400-127358200	Weak transcription	Pancreas	Pancrea
31	chr7:127349600-127357400	Weak transcription	Aorta	Aorta
32	chr7:127349600-127360400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:127349600-127371200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr7:127350600-127358200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:127350800-127355400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr7:127351400-127355000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:127351400-127355200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:127351400-127357600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr7:127351400-127358000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:127351400-127361000	Weak transcription	Ovary	ovary
41	chr7:127351400-127361200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr7:127351400-127362600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr7:127351400-127365800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:127351400-127365800	Strong transcription	HSMM	muscle
45	chr7:127351400-127366200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:127351400-127368400	Weak transcription	Stomach Mucosa	stomach
47	chr7:127351400-127375600	Strong transcription	Liver	Liver
48	chr7:127351400-127383800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr7:127351600-127382200	Strong transcription	K562	blood
50	chr7:127351800-127354800	Strong transcription	Rectal Mucosa Donor 31	rectum

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