Variant report

Variant	rs17134769
Chromosome Location	chr7:108111356-108111357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108110315..108113078-chr7:108114335..108116967,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10953572	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10953573	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11971386	0.83[EUR][1000 genomes]
rs11977071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983802	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11983842	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12530879	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12536929	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12538539	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12540029	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13224588	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16872576	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs16872577	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs34915298	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35220845	0.83[EUR][1000 genomes]
rs35444439	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35687881	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3752639	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3763460	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3763463	0.80[EUR][1000 genomes]
rs6964631	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6980319	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71568524	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71568525	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7786180	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9641410	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9641411	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	esv2753284	chr7:108105345-108130214	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17134769	NRCAM	cis	cerebellum	SCAN
rs17134769	CDHR3	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108097200-108118000	Weak transcription	Aorta	Aorta
2	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:108101000-108119200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr7:108101400-108116800	Weak transcription	Osteobl	bone
5	chr7:108102400-108129600	Weak transcription	Pancreas	Pancrea
6	chr7:108102400-108137000	Weak transcription	NH-A	brain
7	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr7:108102600-108116000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:108102600-108118200	Weak transcription	Fetal Muscle Leg	muscle
10	chr7:108102800-108126400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
12	chr7:108103200-108115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:108104400-108116400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:108104800-108117400	Weak transcription	Dnd41	blood
15	chr7:108105000-108116000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr7:108105600-108117800	Weak transcription	Thymus	Thymus
17	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:108106000-108116800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr7:108106200-108150800	Weak transcription	NHLF	lung
20	chr7:108106400-108113000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:108106400-108117200	Weak transcription	Primary T cells from cord blood	blood
22	chr7:108106600-108127600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr7:108106800-108130000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr7:108107600-108141000	Weak transcription	Spleen	Spleen
25	chr7:108108200-108111400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:108108200-108111600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:108108400-108113400	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:108108600-108122000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:108108800-108118200	Weak transcription	Right Ventricle	heart
30	chr7:108108800-108118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:108109000-108111400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:108109000-108111400	Weak transcription	Liver	Liver
33	chr7:108109000-108112600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:108109000-108117200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:108109000-108119200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:108109000-108126400	Weak transcription	HUVEC	blood vessel
37	chr7:108109000-108129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr7:108109000-108136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:108109000-108141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:108109200-108114400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:108109200-108117000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr7:108109400-108113200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:108109600-108115000	Weak transcription	Primary B cells from cord blood	blood
45	chr7:108109600-108116600	Weak transcription	Placenta	Placenta
46	chr7:108109600-108117000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:108109600-108127600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:108109600-108140600	Weak transcription	Esophagus	oesophagus
49	chr7:108109600-108143400	Weak transcription	GM12878-XiMat	blood
50	chr7:108109800-108111800	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links