Variant report

Variant	rs10947494
Chromosome Location	chr6:34263743-34263744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34261986..34267851-chr6:34269330..34272911,9	K562	blood:
2	chr6:34262225..34265045-chr6:34266800..34268628,2	K562	blood:
3	chr6:34254295..34258176-chr6:34263352..34265255,3	K562	blood:
4	chr6:34263488..34269053-chr6:34269608..34275567,7	K562	blood:

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16894846	1.00[YRI][hapmap]
rs6691	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357177	0.87[AMR][1000 genomes];0.85[EUR][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	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10947494	HLA-DRB5	cis	cerebellum	SCAN
rs10947494	SLC25A24	trans	parietal	SCAN
rs10947494	SPDEF	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:34246000-34264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:34246600-34264000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:34246600-34264000	Strong transcription	Dnd41	blood
6	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:34253600-34271200	Weak transcription	Stomach Mucosa	stomach
8	chr6:34255000-34263800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr6:34255200-34263800	Strong transcription	Fetal Stomach	stomach
10	chr6:34256600-34264400	Weak transcription	Right Atrium	heart
11	chr6:34257000-34264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:34258200-34263800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:34258800-34264600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr6:34259200-34264000	Strong transcription	HepG2	liver
15	chr6:34259400-34263800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:34259400-34263800	Strong transcription	Stomach Smooth Muscle	stomach
17	chr6:34259600-34264600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:34260200-34272800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:34261400-34263800	Weak transcription	A549	lung
20	chr6:34261400-34264400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:34261400-34266800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:34261400-34269000	Weak transcription	NHDF-Ad	bronchial
23	chr6:34261400-34269200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:34261400-34269400	Weak transcription	NHLF	lung
25	chr6:34261400-34273400	Weak transcription	Fetal Kidney	kidney
26	chr6:34261400-34276000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:34261600-34265200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:34261600-34268600	Weak transcription	Brain Substantia Nigra	brain
29	chr6:34261600-34269200	Weak transcription	NH-A	brain
30	chr6:34261600-34269200	Weak transcription	Osteobl	bone
31	chr6:34261600-34273400	Weak transcription	Colon Smooth Muscle	Colon
32	chr6:34261600-34276200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:34261800-34268000	Weak transcription	Placenta	Placenta
34	chr6:34261800-34269200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:34261800-34269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:34261800-34269200	Weak transcription	Brain Germinal Matrix	brain
37	chr6:34261800-34269400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:34261800-34271200	Weak transcription	HUVEC	blood vessel
39	chr6:34261800-34273600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:34261800-34275200	Weak transcription	Aorta	Aorta
41	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:34262000-34264000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr6:34262000-34264200	Weak transcription	Colonic Mucosa	Colon
44	chr6:34262000-34264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:34262000-34264400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr6:34262000-34264400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:34262000-34264400	Weak transcription	HSMMtube	muscle
48	chr6:34262000-34264400	Weak transcription	NHEK	skin
49	chr6:34262000-34265200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:34262000-34267800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links