Variant report

Variant	rs10485029
Chromosome Location	chr6:37799704-37799705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37797940..37799807-chr6:37808764..37811623,2	MCF-7	breast:
2	chr6:37797639..37800200-chr6:37805960..37807518,2	K562	blood:
3	chr6:37786464..37788426-chr6:37798641..37800200,2	K562	blood:

Variant related genes	Relation type
ENSG00000156639	Chromatin interaction
ENSG00000225945	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10456096	0.88[CHB][hapmap]
rs1074234	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947707	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1187421	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1187422	0.91[AFR][1000 genomes]
rs1187423	0.91[AFR][1000 genomes]
rs12190570	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12211248	0.84[AFR][1000 genomes]
rs12211981	0.87[GIH][hapmap]
rs12213835	0.87[GIH][hapmap]
rs2055206	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs259679	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs259686	0.82[CEU][hapmap];0.87[GIH][hapmap]
rs259689	0.87[GIH][hapmap]
rs259713	0.87[GIH][hapmap]
rs259715	0.94[AFR][1000 genomes]
rs259716	0.81[AFR][1000 genomes]
rs259718	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2645117	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2645124	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs2842517	0.87[GIH][hapmap]
rs2842527	1.00[ASW][hapmap];0.96[LWK][hapmap];0.96[YRI][hapmap]
rs34592529	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35806631	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35925070	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711514	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4714120	0.82[MEX][hapmap];0.87[TSI][hapmap]
rs6458027	0.81[AFR][1000 genomes]
rs6458028	0.85[AFR][1000 genomes]
rs6458029	0.88[CHB][hapmap]
rs9296232	0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs9394460	0.93[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];0.83[AFR][1000 genomes]
rs9470706	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10485029	KCNK17	cis	parietal	SCAN
rs10485029	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37789400-37800000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr6:37791000-37800400	Weak transcription	Thymus	Thymus
3	chr6:37791200-37800000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:37791200-37820000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:37791400-37800400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:37791400-37800400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:37791400-37801800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:37791400-37801800	Weak transcription	Fetal Brain Female	brain
9	chr6:37791400-37801800	Weak transcription	A549	lung
10	chr6:37791400-37810200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:37791400-37813400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:37791400-37816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:37791600-37800000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:37791600-37801400	Weak transcription	Brain Germinal Matrix	brain
15	chr6:37792000-37800400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:37792400-37800400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:37792400-37801800	Weak transcription	Fetal Brain Male	brain
18	chr6:37793800-37801600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:37793800-37813600	Weak transcription	NH-A	brain
20	chr6:37794000-37819800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:37794400-37805200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:37794800-37800800	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:37795000-37813800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:37795000-37825600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr6:37795200-37799800	Weak transcription	HepG2	liver
26	chr6:37795800-37802200	Weak transcription	NHLF	lung
27	chr6:37795800-37813400	Weak transcription	HSMMtube	muscle
28	chr6:37796000-37800400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:37796000-37800400	Weak transcription	Fetal Stomach	stomach
30	chr6:37796000-37800600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:37796000-37812800	Weak transcription	Colonic Mucosa	Colon
32	chr6:37796000-37813200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:37796000-37813800	Weak transcription	NHDF-Ad	bronchial
34	chr6:37796000-37815600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:37796000-37828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:37796000-37830600	Weak transcription	Hela-S3	cervix
37	chr6:37796200-37800400	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:37796200-37801600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr6:37796200-37801600	Weak transcription	Fetal Lung	lung
40	chr6:37796200-37801800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:37796200-37801800	Weak transcription	Fetal Kidney	kidney
42	chr6:37796200-37802400	Weak transcription	Fetal Intestine Large	intestine
43	chr6:37796200-37811400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:37796200-37813200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:37796400-37800400	Weak transcription	Fetal Intestine Small	intestine
46	chr6:37796400-37800800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:37796400-37803400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr6:37796800-37800000	Enhancers	Liver	Liver
49	chr6:37796800-37801000	Enhancers	Psoas Muscle	Psoas
50	chr6:37797000-37801000	Enhancers	Spleen	Spleen

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