Variant report

Variant	rs7177949
Chromosome Location	chr15:40677038-40677039
allele	A/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:40675969..40678151-chr15:40728400..40731089,2	K562	blood:
2	chr15:40613571..40616194-chr15:40676591..40679577,2	K562	blood:
3	chr15:40675852..40678402-chr15:40700854..40703282,2	K562	blood:
4	chr15:40676011..40678740-chr15:40696810..40699537,3	MCF-7	breast:
5	chr15:40675487..40678192-chr15:40681200..40683713,3	K562	blood:
6	chr15:40674190..40678981-chr15:40695777..40699659,7	MCF-7	breast:
7	chr15:40675071..40677376-chr15:40697128..40699914,2	K562	blood:
8	chr15:40675097..40677864-chr15:40680611..40684131,5	K562	blood:
9	chr15:40663732..40667062-chr15:40674726..40678158,3	MCF-7	breast:
10	chr15:40675852..40678402-chr15:40700854..40703282,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000128928	Chromatin interaction
ENSG00000259714	Chromatin interaction
ENSG00000261374	Chromatin interaction
ENSG00000128944	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11541641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11541643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12185076	0.94[EUR][1000 genomes]
rs16970653	1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs16970660	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs2229312	0.94[EUR][1000 genomes]
rs28379196	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62018001	0.83[ASN][1000 genomes]
rs6492944	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]
rs68169695	0.94[EUR][1000 genomes]
rs7175153	0.88[YRI][hapmap]
rs7176592	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]
rs72733427	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733428	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72733434	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72733437	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72733442	0.94[EUR][1000 genomes]
rs72733444	0.92[EUR][1000 genomes]
rs72733445	0.90[EUR][1000 genomes]
rs72733449	0.90[EUR][1000 genomes]
rs72733450	0.90[EUR][1000 genomes]
rs72733453	0.90[EUR][1000 genomes]
rs73383135	0.94[EUR][1000 genomes]
rs8031814	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8031994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8032114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8036457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs875767	1.00[CHB][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7177949	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs7177949	C15orf23	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40675000-40677600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:40675800-40677400	Weak transcription	Gastric	stomach
3	chr15:40675800-40678600	Weak transcription	Left Ventricle	heart
4	chr15:40675800-40678800	Weak transcription	Lung	lung
5	chr15:40675800-40678800	Weak transcription	Pancreas	Pancrea
6	chr15:40675800-40679000	Weak transcription	Esophagus	oesophagus
7	chr15:40675800-40679000	Weak transcription	Psoas Muscle	Psoas
8	chr15:40675800-40681200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:40676000-40677800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr15:40676000-40677800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:40676000-40678600	Weak transcription	Aorta	Aorta
12	chr15:40676000-40678600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:40676000-40678800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:40676000-40678800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:40676000-40678800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:40676000-40678800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:40676000-40679000	Weak transcription	Ovary	ovary
18	chr15:40676000-40689800	Weak transcription	Right Atrium	heart
19	chr15:40676000-40697400	Weak transcription	Small Intestine	intestine
20	chr15:40676200-40677200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr15:40676200-40677400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:40676200-40677400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:40676200-40677400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:40676200-40677400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:40676200-40677600	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr15:40676200-40677800	Enhancers	Fetal Heart	heart
27	chr15:40676200-40678000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:40676200-40678400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr15:40676200-40678600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:40676200-40678600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:40676200-40678600	Weak transcription	Brain Anterior Caudate	brain
32	chr15:40676200-40678600	Weak transcription	Fetal Intestine Large	intestine
33	chr15:40676200-40678600	Weak transcription	Fetal Kidney	kidney
34	chr15:40676200-40678800	Weak transcription	Primary B cells from cord blood	blood
35	chr15:40676200-40678800	Weak transcription	Primary T cells from cord blood	blood
36	chr15:40676200-40678800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:40676200-40678800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:40676200-40678800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:40676200-40678800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:40676200-40678800	Weak transcription	Adipose Nuclei	Adipose
41	chr15:40676200-40678800	Weak transcription	Liver	Liver
42	chr15:40676200-40678800	Weak transcription	Brain Substantia Nigra	brain
43	chr15:40676200-40678800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:40676200-40678800	Weak transcription	Fetal Intestine Small	intestine
45	chr15:40676200-40678800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:40676200-40678800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:40676200-40678800	Weak transcription	Spleen	Spleen
48	chr15:40676200-40679000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:40676200-40679000	Weak transcription	Brain Hippocampus Middle	brain
50	chr15:40676200-40679000	Weak transcription	Fetal Brain Male	brain

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