Variant report

Variant	rs460982
Chromosome Location	chr21:40192577-40192578
allele	C/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: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	chr21:40191292..40193852-chr21:40279000..40281951,2	MCF-7	breast:
2	chr21:40191844..40194526-chr21:40280639..40282336,2	MCF-7	breast:
3	chr21:40192244..40193901-chr21:40196829..40198564,2	MCF-7	breast:
4	chr21:40190146..40192879-chr21:40208219..40210251,3	MCF-7	breast:
5	chr21:40191710..40193664-chr21:40199338..40200955,2	MCF-7	breast:
6	chr21:40192057..40193677-chr21:40201859..40203511,2	MCF-7	breast:
7	chr21:40190407..40192977-chr21:40211375..40214122,2	MCF-7	breast:
8	chr21:40191810..40193575-chr21:40211576..40213668,2	K562	blood:

No data

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1209952	0.80[CEU][hapmap]
rs1209954	0.87[CEU][hapmap];0.85[TSI][hapmap]
rs2070529	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2070530	1.00[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2836701	0.89[GIH][hapmap]
rs2836706	0.87[GIH][hapmap]
rs457705	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs459411	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs460475	0.80[GIH][hapmap]
rs461155	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs467940	0.80[GIH][hapmap]
rs467985	0.80[GIH][hapmap]
rs468094	0.91[EUR][1000 genomes]
rs468837	0.82[GIH][hapmap]

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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs460982	KCNJ6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40180200-40198400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr21:40181600-40192600	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr21:40181600-40193600	Strong transcription	Fetal Muscle Leg	muscle
4	chr21:40181800-40193800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr21:40181800-40197000	Strong transcription	Fetal Thymus	thymus
6	chr21:40182000-40196600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr21:40183000-40196600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr21:40183600-40196800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr21:40183800-40196800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:40184000-40192600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr21:40184000-40193600	Strong transcription	Primary hematopoietic stem cells	blood
12	chr21:40184000-40196800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr21:40184200-40193200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr21:40184400-40196800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:40184600-40195000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr21:40184600-40196000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr21:40184800-40195200	Strong transcription	Ovary	ovary
18	chr21:40184800-40196600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr21:40184800-40196800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr21:40185000-40192600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr21:40185000-40192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr21:40185000-40196600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr21:40185000-40196600	Strong transcription	K562	blood
24	chr21:40185000-40197000	Strong transcription	Thymus	Thymus
25	chr21:40185200-40196600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr21:40185400-40193600	Weak transcription	Brain Germinal Matrix	brain
27	chr21:40185400-40194000	Strong transcription	Fetal Intestine Large	intestine
28	chr21:40185600-40195200	Weak transcription	Fetal Brain Female	brain
29	chr21:40185600-40195200	Strong transcription	GM12878-XiMat	blood
30	chr21:40185800-40193200	Strong transcription	Fetal Stomach	stomach
31	chr21:40186000-40197600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr21:40186200-40195800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr21:40186200-40196400	Strong transcription	Primary B cells from cord blood	blood
34	chr21:40186200-40197000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr21:40186400-40194400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr21:40186400-40195200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr21:40186400-40195200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr21:40186600-40194800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr21:40186600-40196600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr21:40186600-40196800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr21:40186800-40192600	Weak transcription	Right Atrium	heart
42	chr21:40186800-40196600	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr21:40186800-40196600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr21:40186800-40196800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr21:40187000-40192600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr21:40187000-40195200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr21:40187000-40196800	Genic enhancers	Rectal Mucosa Donor 31	rectum
48	chr21:40187000-40197400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr21:40187000-40197400	Strong transcription	Dnd41	blood
50	chr21:40187200-40194000	Strong transcription	Fetal Intestine Small	intestine

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