Variant report

Variant	rs16972767
Chromosome Location	chr19:39153044-39153045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39150052..39153067-chr19:39197622..39201361,3	MCF-7	breast:
2	chr19:39152656..39156169-chr19:39159383..39162487,4	K562	blood:
3	chr19:39151862..39154243-chr19:39220891..39223454,2	MCF-7	breast:
4	chr19:39150956..39153225-chr19:39190082..39192763,2	MCF-7	breast:
5	chr19:39151900..39153408-chr19:39203433..39205156,2	MCF-7	breast:
6	chr19:39145586..39147740-chr19:39150423..39154465,3	K562	blood:
7	chr19:39136583..39139247-chr19:39152891..39155036,2	K562	blood:
8	chr19:39150082..39153309-chr19:39178166..39180062,3	MCF-7	breast:
9	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
10	chr19:39151502..39153525-chr19:39175124..39177403,2	MCF-7	breast:
11	chr19:39141727..39145361-chr19:39153035..39156463,3	K562	blood:
12	chr19:39152968..39155649-chr19:39189504..39191382,2	MCF-7	breast:
13	chr19:39151359..39154098-chr19:39320807..39323487,3	MCF-7	breast:
14	chr19:39152027..39154763-chr19:39201126..39202967,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104823	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10403540	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10404257	0.92[ASN][1000 genomes]
rs10406778	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10415219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10415646	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10421560	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10426809	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs11083475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12460849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12462270	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13343794	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13344413	0.96[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2279144	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2303040	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28488032	0.85[ASN][1000 genomes]
rs28624276	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3745859	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786839	1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs3786845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786848	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3786851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810341	0.99[ASN][1000 genomes]
rs55876653	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56113315	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56365761	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62121814	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62121816	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121818	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7251903	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs7252589	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7254100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8107416	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs8111746	0.84[ASN][1000 genomes]
rs883394	0.81[EUR][1000 genomes]
rs883433	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs979971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs979972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16972767	LGALS17A	cis	cerebellum	SCAN
rs16972767	PSG3	cis	parietal	SCAN
rs16972767	ZNF526	cis	cerebellum	SCAN
rs16972767	ERCC1	cis	cerebellum	SCAN
rs16972767	MEGF8	cis	parietal	SCAN
rs16972767	RPS16	cis	parietal	SCAN
rs16972767	TMEM145	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39143400-39154400	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr19:39143800-39153200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr19:39144200-39153400	Genic enhancers	K562	blood
5	chr19:39144600-39154000	Enhancers	Right Atrium	heart
6	chr19:39144800-39154000	Genic enhancers	Fetal Intestine Large	intestine
7	chr19:39145200-39153400	Genic enhancers	Fetal Intestine Small	intestine
8	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:39147600-39154000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:39147600-39154000	Enhancers	Brain Angular Gyrus	brain
11	chr19:39147800-39160800	Enhancers	Placenta	Placenta
12	chr19:39148600-39153400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
13	chr19:39149000-39154200	Enhancers	Brain Substantia Nigra	brain
14	chr19:39149000-39154600	Weak transcription	Primary T cells from cord blood	blood
15	chr19:39149000-39155200	Weak transcription	Fetal Brain Female	brain
16	chr19:39149200-39153400	Genic enhancers	Fetal Muscle Leg	muscle
17	chr19:39149600-39153200	Weak transcription	Brain Germinal Matrix	brain
18	chr19:39149600-39154000	Enhancers	Brain Hippocampus Middle	brain
19	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
20	chr19:39150000-39157600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
21	chr19:39150200-39154200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr19:39150400-39153200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:39150400-39153600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr19:39150400-39154400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:39150400-39155000	Genic enhancers	HMEC	breast
26	chr19:39150600-39154600	Genic enhancers	Osteobl	bone
27	chr19:39150800-39154400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:39150800-39155000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:39151000-39154400	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr19:39151000-39154600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:39151200-39153200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
32	chr19:39151200-39153200	Genic enhancers	NH-A	brain
33	chr19:39151200-39154800	Genic enhancers	HepG2	liver
34	chr19:39151200-39155800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr19:39151200-39157600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:39151200-39157600	Genic enhancers	Fetal Stomach	stomach
37	chr19:39151400-39153200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:39151400-39154400	Genic enhancers	HSMM	muscle
39	chr19:39151400-39155200	Genic enhancers	HSMMtube	muscle
40	chr19:39151400-39156200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:39151400-39157400	Genic enhancers	NHLF	lung
42	chr19:39151400-39160000	Enhancers	H9 Cell Line	embryonic stem cell
43	chr19:39151600-39153200	Strong transcription	GM12878-XiMat	blood
44	chr19:39151600-39153400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:39151600-39153400	Transcr. at gene 5' and 3'	NHEK	skin
46	chr19:39151600-39154200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:39151600-39154200	Enhancers	Brain Anterior Caudate	brain
48	chr19:39151800-39156800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:39152000-39153200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr19:39152000-39153400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links