Variant report

Variant	rs6539164
Chromosome Location	chr12:104997370-104997371
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104995437..104998034-chr12:105005195..105009191,4	K562	blood:
2	chr12:104989262..104996194-chr12:104996249..105001190,9	K562	blood:
3	chr12:104995476..104999568-chr12:105000294..105003603,4	MCF-7	breast:
4	chr12:104877368..104879475-chr12:104994945..104997533,2	K562	blood:
5	chr12:104996638..104999382-chr12:105016902..105018701,2	K562	blood:
6	chr12:104850509..104852639-chr12:104996594..104998975,2	MCF-7	breast:
7	chr12:104996399..104998456-chr12:105002964..105004800,2	K562	blood:
8	chr12:104995437..104998034-chr12:105002964..105009191,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000171310	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10746004	1.00[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs10778342	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162661	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2888827	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3812796	0.94[CEU][hapmap];0.81[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs6539162	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539163	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972130	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1035364	chr12:104948307-105003705	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6539164	CRY1	cis	parietal	SCAN
rs6539164	UTP20	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104980200-104997600	Weak transcription	Esophagus	oesophagus
2	chr12:104983200-104997800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:104987800-104997800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:104989200-104997800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:104989400-104997800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr12:104989400-105030600	Strong transcription	Dnd41	blood
7	chr12:104990800-104997600	Weak transcription	Brain Angular Gyrus	brain
8	chr12:104991000-104997600	Weak transcription	Left Ventricle	heart
9	chr12:104991000-104997600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:104991000-104997800	Weak transcription	Aorta	Aorta
11	chr12:104991400-104997600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:104991600-104998000	Weak transcription	Fetal Kidney	kidney
13	chr12:104991800-104997600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:104992200-104997400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:104992400-104997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:104992800-104997400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:104992800-104997800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:104993000-104997600	Weak transcription	Right Ventricle	heart
19	chr12:104993200-104997600	Weak transcription	Small Intestine	intestine
20	chr12:104993200-104999400	Weak transcription	Brain Germinal Matrix	brain
21	chr12:104993200-105006200	Weak transcription	Fetal Heart	heart
22	chr12:104993200-105012600	Weak transcription	Gastric	stomach
23	chr12:104993400-104999600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:104993600-104997600	Enhancers	NHDF-Ad	bronchial
25	chr12:104993800-104997600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:104993800-104998000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:104994200-104997800	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:104994800-104997400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr12:104994800-104997600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:104995000-104997400	Weak transcription	Adipose Nuclei	Adipose
31	chr12:104995200-104997600	Enhancers	HUVEC	blood vessel
32	chr12:104995200-104997800	Enhancers	NHEK	skin
33	chr12:104995200-104998200	Enhancers	HMEC	breast
34	chr12:104995400-104997400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:104995400-104997800	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr12:104995400-104998800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:104995400-105000000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:104995600-104997400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:104995600-104997400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:104995600-104997400	Strong transcription	Primary B cells from cord blood	blood
41	chr12:104995600-104997400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr12:104995600-104997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:104995600-104997600	Weak transcription	Brain Substantia Nigra	brain
44	chr12:104995600-104997600	Weak transcription	Pancreas	Pancrea
45	chr12:104995600-104997800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:104995600-104997800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:104995600-104997800	Weak transcription	Colonic Mucosa	Colon
48	chr12:104995600-104998000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:104995800-104997400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr12:104995800-104997400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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