Variant report

Variant	rs17151507
Chromosome Location	chr7:127541656-127541657
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr7:127541611-127541937	GM12878	blood:	n/a	n/a
2	ATF2	chr7:127541397-127542428	GM12878	blood:	n/a	n/a
3	TEAD4	chr7:127541307-127541681	H1-hESC	embryonic stem cell:	n/a	n/a
4	USF2	chr7:127541502-127541724	GM12878	blood:	n/a	n/a
5	RUNX3	chr7:127541372-127542377	GM12878	blood:	n/a	n/a
6	STAT1	chr7:127541581-127541726	GM12878	blood:	n/a	n/a
7	NFIC	chr7:127541230-127541742	GM12878	blood:	n/a	n/a
8	RUNX3	chr7:127541434-127542362	GM12878	blood:	n/a	n/a
9	EBF1	chr7:127541464-127542281	GM12878	blood:	n/a	n/a
10	BHLHE40	chr7:127541557-127541757	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127539859..127542368-chr7:127543054..127544559,2	K562	blood:
2	chr7:127535349..127538608-chr7:127539437..127541786,4	MCF-7	breast:
3	chr7:127530901..127533766-chr7:127540275..127542321,2	K562	blood:
4	chr7:127539496..127544017-chr7:127546415..127549727,4	MCF-7	breast:
5	chr7:127540563..127543536-chr7:127545716..127548575,3	K562	blood:
6	chr7:127540989..127542676-chr7:127542945..127545682,2	MCF-7	breast:

No data

Variant related genes	Relation type
SND1	TF binding region
ENSG00000197157	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10487499	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487502	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155421	1.00[ASN][1000 genomes]
rs12375023	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531847	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532894	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534918	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537331	0.85[GIH][hapmap];1.00[MEX][hapmap]
rs12540357	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706816	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706818	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706819	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12706820	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706822	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706823	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221709	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227201	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229973	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231367	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13246286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345283	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348103	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1362898	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468701	0.98[EUR][1000 genomes]
rs17151466	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151639	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs17151653	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151668	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17151682	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17151707	0.89[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs17151739	0.85[GIH][hapmap];0.93[MEX][hapmap]
rs17676654	1.00[ASN][1000 genomes]
rs34026100	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688920	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34839191	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35154268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41464647	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs55660321	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58406876	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58489175	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6467157	1.00[CHB][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];1.00[ASN][1000 genomes]
rs67632185	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67827668	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6948605	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953231	1.00[CHB][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs6959487	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962635	1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes]
rs73232968	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73232972	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73234873	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73234874	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73238078	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs741094	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7458839	0.99[EUR][1000 genomes]
rs7785596	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805021	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809182	1.00[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.99[EUR][1000 genomes]
rs7810024	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894062	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649027	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9649512	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv526535	chr7:127445594-127623840	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17151507	SND1	cis	Artery Tibial	GTEx
rs17151507	ARF5	cis	cerebellum	SCAN
rs17151507	HYAL4	cis	cerebellum	SCAN
rs17151507	GPR37	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127505800-127542000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:127526200-127544600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:127528800-127569200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr7:127529000-127557200	Weak transcription	Esophagus	oesophagus
5	chr7:127529200-127544600	Weak transcription	Thymus	Thymus
6	chr7:127529200-127545600	Weak transcription	Fetal Stomach	stomach
7	chr7:127529200-127546200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:127529200-127548400	Weak transcription	Right Ventricle	heart
9	chr7:127529200-127569400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:127529400-127542200	Weak transcription	Fetal Heart	heart
11	chr7:127529400-127551000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:127531800-127542000	Weak transcription	Fetal Kidney	kidney
13	chr7:127532200-127569200	Weak transcription	Hela-S3	cervix
14	chr7:127532400-127547400	Weak transcription	A549	lung
15	chr7:127532400-127569200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr7:127532600-127546000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:127532800-127544800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:127532800-127545600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr7:127534000-127542200	Weak transcription	Adipose Nuclei	Adipose
20	chr7:127534400-127544400	Weak transcription	Fetal Brain Male	brain
21	chr7:127535000-127542600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr7:127535000-127543200	Enhancers	Fetal Intestine Large	intestine
23	chr7:127535800-127542800	Enhancers	Fetal Intestine Small	intestine
24	chr7:127538000-127542600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr7:127538200-127542200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:127538200-127542800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr7:127538200-127544200	Weak transcription	NHEK	skin
28	chr7:127538400-127544600	Weak transcription	NHDF-Ad	bronchial
29	chr7:127538400-127545400	Weak transcription	HSMM	muscle
30	chr7:127538400-127546000	Weak transcription	NHLF	lung
31	chr7:127538600-127544000	Weak transcription	HMEC	breast
32	chr7:127538600-127544400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:127538800-127544600	Weak transcription	HSMMtube	muscle
34	chr7:127538800-127546200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:127539000-127544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:127539000-127544400	Weak transcription	HUVEC	blood vessel
37	chr7:127539000-127545600	Weak transcription	NH-A	brain
38	chr7:127539000-127556400	Weak transcription	Psoas Muscle	Psoas
39	chr7:127539200-127544600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:127539400-127542600	Enhancers	H9 Cell Line	embryonic stem cell
41	chr7:127539600-127541800	Enhancers	Small Intestine	intestine
42	chr7:127539600-127542600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr7:127539600-127542800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr7:127539600-127544600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr7:127539800-127541800	Genic enhancers	K562	blood
46	chr7:127539800-127542600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr7:127539800-127542600	Enhancers	Brain Anterior Caudate	brain
48	chr7:127539800-127542600	Enhancers	Duodenum Mucosa	Duodenum
49	chr7:127539800-127542800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:127539800-127544800	Enhancers	H1 Cell Line	embryonic stem cell

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