Variant report

Variant	rs6715929
Chromosome Location	chr2:172877507-172877508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172857904..172859439-chr2:172876035..172878668,2	K562	blood:
2	chr2:172860017..172861984-chr2:172875793..172878198,2	K562	blood:
3	chr2:172875314..172877741-chr2:172963379..172965447,2	MCF-7	breast:
4	chr2:172864480..172870614-chr2:172875986..172878962,8	K562	blood:
5	chr2:172874695..172877681-chr2:172884146..172886439,2	K562	blood:
6	chr2:172862481..172869340-chr2:172872333..172878575,9	MCF-7	breast:
7	chr2:172870841..172873802-chr2:172876022..172878107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10165126	0.87[ASW][hapmap];0.84[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs10166548	0.84[EUR][1000 genomes]
rs10174055	0.96[CEU][hapmap];0.92[TSI][hapmap]
rs10201053	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10202823	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs10930502	0.92[CEU][hapmap]
rs12692978	0.80[ASW][hapmap]
rs3063041	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770445	0.80[ASW][hapmap]
rs4668414	0.83[CEU][hapmap]
rs6433319	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs6724337	0.80[ASW][hapmap];0.83[CEU][hapmap]
rs6725388	0.88[CEU][hapmap]
rs6727017	0.92[CEU][hapmap]
rs6731562	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs6737308	0.81[CEU][hapmap]
rs6752812	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs6759575	0.80[ASW][hapmap];0.83[CEU][hapmap]
rs7573003	0.83[CEU][hapmap]
rs908670	0.80[ASW][hapmap]

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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv3031	chr2:172867462-172884232	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6715929	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6715929	AC068039.4	cis	Whole Blood	GTEx
rs6715929	AC068039.4	cis	lung	GTEx
rs6715929	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6715929	AC068039.4	cis	Thyroid	GTEx
rs6715929	SLC25A12	cis	cerebellum	SCAN
rs6715929	FASTKD1	cis	parietal	SCAN
rs6715929	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6715929	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6715929	SLC25A12	cis	parietal	SCAN
rs6715929	AC068039.4	cis	Muscle Skeletal	GTEx
rs6715929	DYNC1I2	cis	cerebellum	SCAN
rs6715929	SLC25A12	cis	Whole Blood	GTEx
rs6715929	MYO3B	cis	cerebellum	SCAN
rs6715929	AC068039.4	cis	Stomach	GTEx
rs6715929	AC068039.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172865200-172886600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:172865400-172878000	Weak transcription	Gastric	stomach
3	chr2:172865600-172878000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:172865600-172897400	Weak transcription	Primary T cells from cord blood	blood
5	chr2:172865800-172877600	Weak transcription	Fetal Kidney	kidney
6	chr2:172865800-172878000	Weak transcription	Primary B cells from cord blood	blood
7	chr2:172865800-172886400	Weak transcription	Fetal Intestine Small	intestine
8	chr2:172865800-172886600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:172866000-172877600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:172866000-172877800	Weak transcription	HSMM	muscle
11	chr2:172866000-172878000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:172866000-172886800	Weak transcription	HSMMtube	muscle
13	chr2:172866800-172882600	Weak transcription	K562	blood
14	chr2:172874000-172877800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:172874200-172878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:172874200-172886400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:172875000-172878000	Weak transcription	HMEC	breast
18	chr2:172875200-172878800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:172875800-172877600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr2:172875800-172877600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:172875800-172879200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:172876400-172877600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:172876400-172877800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr2:172876400-172878000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:172876400-172878000	Enhancers	Dnd41	blood
26	chr2:172876400-172878800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:172876600-172877600	Enhancers	Primary hematopoietic stem cells	blood
28	chr2:172876600-172877600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:172876600-172877800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:172876600-172878800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr2:172876800-172878600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr2:172876800-172878600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr2:172876800-172878800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr2:172877000-172877600	Enhancers	Fetal Muscle Leg	muscle
35	chr2:172877000-172878200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr2:172877000-172878200	Enhancers	Brain Germinal Matrix	brain
37	chr2:172877000-172878200	Enhancers	GM12878-XiMat	blood
38	chr2:172877000-172878600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:172877000-172878600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr2:172877000-172878600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr2:172877000-172878600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr2:172877000-172878800	Enhancers	H1 Cell Line	embryonic stem cell
43	chr2:172877000-172878800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:172877000-172878800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:172877000-172878800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr2:172877200-172877800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:172877200-172878400	Enhancers	Fetal Brain Male	brain
48	chr2:172877200-172878400	Enhancers	HepG2	liver
49	chr2:172877200-172878600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:172877200-172878600	Enhancers	Fetal Brain Female	brain

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