Variant report

Variant	rs894062
Chromosome Location	chr7:127291266-127291267
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	CEBPB	chr7:127291152-127291442	K562	blood:	n/a	n/a
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	MYC	chr7:127291004-127293350	K562	blood:	n/a	chr7:127293151-127293161 chr7:127291654-127291663 chr7:127292615-127292625
5	MAX	chr7:127291214-127292747	NB4	blood:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
6	CTCF	chr7:127291240-127291390	GM12864	blood:	n/a	n/a
7	ZMIZ1	chr7:127291131-127292885	K562	blood:	n/a	n/a
8	MYC	chr7:127291168-127293291	K562	blood:	n/a	chr7:127293151-127293161 chr7:127291654-127291663 chr7:127292615-127292625
9	POLR2A	chr7:127291188-127292540	K562	blood:	n/a	n/a
10	POLR2A	chr7:127290908-127292823	K562	blood:	n/a	n/a
11	POLR2A	chr7:127291231-127293124	K562	blood:	n/a	n/a
12	MTA3	chr7:127290837-127293079	GM12878	blood:	n/a	n/a
13	E2F6	chr7:127291053-127292983	K562	blood:	n/a	chr7:127291641-127291655
14	HEY1	chr7:127291193-127292089	K562	blood:	n/a	n/a
15	CHD1	chr7:127291202-127293127	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:127291230-127292753	K562	blood:	n/a	n/a
17	POLR2A	chr7:127291102-127292793	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr7:127291000-127292910	GM19099	blood:	n/a	n/a
19	MYC	chr7:127291204-127292563	A549	lung:	n/a	chr7:127291654-127291663
20	POLR2A	chr7:127290939-127293541	GM12891	blood:	n/a	n/a
21	POLR2A	chr7:127291137-127293028	HUVEC	blood vessel:	n/a	n/a
22	MAX	chr7:127291238-127292748	H1-hESC	embryonic stem cell:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
23	POLR2A	chr7:127290810-127292772	HCT-116	colon:	n/a	n/a
24	POLR2A	chr7:127291080-127293231	K562	blood:	n/a	n/a
25	POLR2A	chr7:127291119-127292717	Hela-S3	cervix:	n/a	n/a
26	MAX	chr7:127291258-127292648	A549	lung:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
27	POLR2A	chr7:127290900-127293179	HCT-116	colon:	n/a	n/a
28	TBL1XR1	chr7:127291257-127292491	GM12878	blood:	n/a	n/a
29	TEAD4	chr7:127291121-127293692	K562	blood:	n/a	n/a
30	CTCF	chr7:127291231-127291423	GM12878	blood:	n/a	chr7:127291405-127291418
31	TRIM28	chr7:127291089-127293581	K562	blood:	n/a	n/a
32	POLR2A	chr7:127291169-127292930	HL-60	blood:	n/a	n/a
33	IRF1	chr7:127291256-127293209	K562	blood:	n/a	chr7:127292920-127292927 chr7:127292111-127292125
34	HCFC1	chr7:127291224-127293305	Hela-S3	cervix:	n/a	n/a
35	MAX	chr7:127291016-127292830	A549	lung:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
36	POLR2A	chr7:127291018-127292793	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:127291092-127293206	K562	blood:	n/a	n/a
38	RELA	chr7:127291160-127292558	GM18951	blood:	n/a	n/a
39	CREB1	chr7:127291183-127292597	GM12878	blood:	n/a	n/a
40	MXI1	chr7:127291236-127292796	H1-hESC	embryonic stem cell:	n/a	n/a
41	HA-E2F1	chr7:127291182-127292825	MCF-7	breast:	n/a	chr7:127291641-127291655
42	TAF1	chr7:127291218-127292564	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr7:127291081-127293542	K562	blood:	n/a	n/a
44	POLR2A	chr7:127290767-127292914	GM12892	blood:	n/a	n/a
45	ATF2	chr7:127291168-127292110	H1-hESC	embryonic stem cell:	n/a	chr7:127291969-127291983
46	USF2	chr7:127291255-127291648	K562	blood:	n/a	n/a
47	TBL1XR1	chr7:127291147-127292454	K562	blood:	n/a	n/a
48	CTCF	chr7:127291200-127291350	SAEC	small airway:	n/a	n/a
49	MAZ	chr7:127291220-127292868	IMR90	lung:	n/a	chr7:127291654-127291663 chr7:127292615-127292625
50	POLR2A	chr7:127291074-127292571	U87	brain:	n/a	n/a

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	chr7:127224289..127226040-chr7:127290840..127293019,2	MCF-7	breast:
4	chr7:127291173..127294029-chr7:127587944..127590935,2	MCF-7	breast:
5	chr7:127223375..127232960-chr7:127286940..127295803,24	K562	blood:
6	chr7:127268675..127271053-chr7:127289533..127291398,3	MCF-7	breast:
7	chr7:127029920..127034279-chr7:127291168..127294285,4	MCF-7	breast:
8	chr7:127029926..127034103-chr7:127290516..127296284,10	K562	blood:
9	chr7:127290259..127292033-chr7:127774841..127777045,2	K562	blood:
10	chr7:127226125..127229974-chr7:127289784..127293571,8	MCF-7	breast:
11	chr7:127028627..127034604-chr7:127290902..127294330,10	K562	blood:
12	chr7:127232149..127233978-chr7:127290816..127293700,2	MCF-7	breast:
13	chr7:127226810..127231119-chr7:127290066..127293801,4	MCF-7	breast:

Variant related genes	Relation type
SND1	TF binding region
ENSG00000048405	Chromatin interaction
ENSG00000179562	Chromatin interaction
ENSG00000004059	Chromatin interaction
ENSG00000106328	Chromatin interaction
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12375023	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540357	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706816	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12706820	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706821	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221709	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236338	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	1.00[ASN][1000 genomes]
rs1348103	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.85[EUR][1000 genomes]
rs17151466	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151507	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327508	1.00[ASN][1000 genomes]
rs34026100	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	1.00[ASN][1000 genomes]
rs34839191	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154268	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35660964	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406876	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67632185	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959487	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73234874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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];1.00[ASN][1000 genomes]
rs9649027	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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
rs894062	SND1	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127290800-127291800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:127290800-127291800	Flanking Active TSS	K562	blood
3	chr7:127290800-127292600	Active TSS	Primary T cells from cord blood	blood
4	chr7:127290800-127294000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr7:127290800-127294000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr7:127291000-127291400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:127291000-127291400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:127291000-127291400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:127291000-127291400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr7:127291000-127291400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr7:127291000-127291400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:127291000-127291400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr7:127291000-127291400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:127291000-127291400	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr7:127291000-127291400	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr7:127291000-127291400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr7:127291000-127291400	Flanking Active TSS	Thymus	Thymus
18	chr7:127291000-127291400	Enhancers	Spleen	Spleen
19	chr7:127291000-127291600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:127291000-127291600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:127291000-127291600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr7:127291000-127291600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr7:127291000-127291600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:127291000-127291600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr7:127291000-127291600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:127291000-127291600	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr7:127291000-127291600	Flanking Active TSS	Fetal Stomach	stomach
28	chr7:127291000-127291600	Flanking Active TSS	Hela-S3	cervix
29	chr7:127291000-127291600	Flanking Active TSS	HMEC	breast
30	chr7:127291000-127291800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr7:127291000-127291800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr7:127291000-127291800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr7:127291000-127291800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr7:127291000-127291800	Flanking Active TSS	Fetal Heart	heart
35	chr7:127291000-127291800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr7:127291000-127291800	Flanking Active TSS	GM12878-XiMat	blood
37	chr7:127291000-127291800	Flanking Active TSS	HepG2	liver
38	chr7:127291000-127291800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr7:127291000-127291800	Flanking Active TSS	Osteobl	bone
40	chr7:127291000-127292000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:127291000-127292600	Active TSS	Brain Anterior Caudate	brain
42	chr7:127291000-127292600	Active TSS	Brain Germinal Matrix	brain
43	chr7:127291000-127292600	Active TSS	Brain Substantia Nigra	brain
44	chr7:127291000-127292600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr7:127291000-127292800	Active TSS	Colon Smooth Muscle	Colon
46	chr7:127291000-127293000	Active TSS	Liver	Liver
47	chr7:127291000-127293000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr7:127291000-127293000	Active TSS	Stomach Smooth Muscle	stomach
49	chr7:127291000-127293200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:127291000-127293200	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links