Variant report

Variant	rs973009
Chromosome Location	chr19:39174332-39174333
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:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39173346..39178089-chr19:39336778..39344017,10	MCF-7	breast:
2	chr19:39173836..39175126-chr19:39204742..39205750,26	MCF-7	breast:
3	chr19:39142774..39144585-chr19:39172676..39174844,2	MCF-7	breast:
4	chr19:39165775..39169288-chr19:39170285..39176842,12	K562	blood:
5	chr19:39173386..39176370-chr19:39183881..39186257,2	MCF-7	breast:
6	chr19:39174035..39174587-chr19:39205052..39205776,2	MCF-7	breast:
7	chr19:39161055..39163275-chr19:39172924..39175598,3	K562	blood:
8	chr19:39166293..39168892-chr19:39172787..39174443,3	MCF-7	breast:
9	chr19:39173836..39175021-chr19:39204742..39205755,40	MCF-7	breast:
10	chr19:38924094..38925883-chr19:39174179..39175718,2	K562	blood:
11	chr19:39169983..39173495-chr19:39173704..39177059,4	K562	blood:
12	chr19:39173652..39177308-chr19:39222608..39229132,8	K562	blood:
13	chr19:39174226..39174870-chr19:39222140..39222657,2	MCF-7	breast:
14	chr19:39173657..39176403-chr19:39201609..39205956,8	MCF-7	breast:
15	chr19:39173031..39174983-chr19:39187946..39191555,3	MCF-7	breast:
16	chr19:39174048..39176701-chr19:39326836..39329387,2	MCF-7	breast:
17	chr19:39127720..39130630-chr19:39171842..39174626,3	MCF-7	breast:
18	chr19:39173858..39174895-chr19:39204828..39205582,8	MCF-7	breast:
19	chr19:39173021..39174655-chr19:39220588..39222676,2	MCF-7	breast:
20	chr19:39172995..39175158-chr19:39322358..39324383,2	MCF-7	breast:
21	chr19:39137186..39142048-chr19:39173514..39178711,9	MCF-7	breast:
22	chr19:39173130..39177008-chr19:39180898..39185286,5	K562	blood:
23	chr19:39137008..39140489-chr19:39173171..39177881,5	K562	blood:
24	chr19:39173711..39176209-chr19:39338739..39340775,2	MCF-7	breast:
25	chr19:39173691..39176634-chr19:39320748..39323238,2	MCF-7	breast:
26	chr19:39122468..39125007-chr19:39173104..39174996,2	MCF-7	breast:
27	chr19:39169995..39171948-chr19:39172735..39174419,2	MCF-7	breast:
28	chr19:39147229..39149429-chr19:39172961..39174850,2	K562	blood:
29	chr19:39140411..39144509-chr19:39172304..39176724,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267892	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000267375	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12971309	0.81[ASN][1000 genomes]
rs12972987	0.88[CHD][hapmap];0.81[MEX][hapmap]
rs12972997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2287728	0.88[CHD][hapmap];0.81[MEX][hapmap]
rs2368524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34105297	0.81[ASN][1000 genomes]
rs34126343	0.81[ASN][1000 genomes]
rs34368672	0.81[ASN][1000 genomes]
rs34525537	0.84[ASN][1000 genomes]
rs34558140	0.84[ASN][1000 genomes]
rs34592527	0.81[ASN][1000 genomes]
rs34695688	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs34862518	0.81[ASN][1000 genomes]
rs34899634	0.81[ASN][1000 genomes]
rs35074956	0.81[ASN][1000 genomes]
rs35685980	0.81[ASN][1000 genomes]
rs35691365	0.84[ASN][1000 genomes]
rs35716073	0.81[ASN][1000 genomes]
rs35941349	0.81[ASN][1000 genomes]
rs3786840	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4491650	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs57230275	0.81[ASN][1000 genomes]
rs60454376	0.81[ASN][1000 genomes]
rs62119101	0.81[ASN][1000 genomes]
rs62119102	0.81[ASN][1000 genomes]
rs62119103	0.81[ASN][1000 genomes]
rs62121819	0.84[ASN][1000 genomes]
rs62121821	0.90[ASN][1000 genomes]
rs62121827	0.81[ASN][1000 genomes]
rs62121829	0.81[ASN][1000 genomes]
rs732135	0.88[CHD][hapmap];0.81[MEX][hapmap]
rs8103530	0.84[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	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
6	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Migraine with aura	23793025	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs973009	TMEM145	cis	parietal	SCAN
rs973009	ERCC2	cis	parietal	SCAN
rs973009	SLC1A5	cis	parietal	SCAN
rs973009	MED29	cis	cerebellum	SCAN
rs973009	SELV	cis	parietal	SCAN
rs973009	CEACAM4	cis	cerebellum	SCAN
rs973009	MED29	cis	parietal	SCAN
rs973009	CEACAM4	cis	parietal	SCAN
rs973009	CEACAM20	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39161200-39176000	Weak transcription	Fetal Brain Male	brain
2	chr19:39161200-39176000	Weak transcription	Fetal Brain Female	brain
3	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
4	chr19:39164600-39178200	Enhancers	Primary T cells fromperipheralblood	blood
5	chr19:39164800-39177600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr19:39164800-39179200	Enhancers	Pancreas	Pancrea
7	chr19:39164800-39179800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr19:39164800-39183800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:39165400-39178200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:39166000-39178200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:39167200-39175600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr19:39167400-39174400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:39167400-39180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:39167800-39175200	Weak transcription	Primary T cells from cord blood	blood
15	chr19:39168400-39177400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39169200-39181000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr19:39170000-39177400	Enhancers	Liver	Liver
18	chr19:39170000-39183400	Enhancers	Placenta	Placenta
19	chr19:39170200-39176800	Weak transcription	Thymus	Thymus
20	chr19:39170200-39177600	Enhancers	Primary hematopoietic stem cells	blood
21	chr19:39170200-39180000	Enhancers	Adipose Nuclei	Adipose
22	chr19:39170800-39174400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr19:39171200-39176800	Genic enhancers	Fetal Muscle Leg	muscle
24	chr19:39171400-39174400	Enhancers	Fetal Heart	heart
25	chr19:39171800-39174800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
26	chr19:39171800-39178200	Enhancers	Psoas Muscle	Psoas
27	chr19:39172200-39175800	Enhancers	Duodenum Mucosa	Duodenum
28	chr19:39172400-39178200	Enhancers	Left Ventricle	heart
29	chr19:39172400-39178200	Enhancers	Spleen	Spleen
30	chr19:39172800-39178000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr19:39173000-39174400	Genic enhancers	GM12878-XiMat	blood
32	chr19:39173000-39174600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr19:39173000-39177400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:39173000-39177400	Enhancers	Brain Anterior Caudate	brain
35	chr19:39173000-39177600	Enhancers	Esophagus	oesophagus
36	chr19:39173000-39177800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr19:39173000-39177800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:39173000-39178000	Enhancers	Fetal Thymus	thymus
39	chr19:39173000-39178000	Enhancers	Small Intestine	intestine
40	chr19:39173000-39178200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:39173000-39180200	Enhancers	NHDF-Ad	bronchial
42	chr19:39173200-39174800	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr19:39173200-39176800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:39173200-39177000	Genic enhancers	Fetal Stomach	stomach
45	chr19:39173200-39177400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr19:39173200-39177400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr19:39173200-39177600	Enhancers	Primary B cells from cord blood	blood
48	chr19:39173200-39178000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:39173200-39179800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:39173400-39174600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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