Variant report

Variant	rs1044677
Chromosome Location	chr12:50260825-50260826
allele	A/G
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50260597..50261524-chr12:50339077..50340027,4	K562	blood:
2	chr12:50260711..50261527-chr12:50464112..50464811,2	MCF-7	breast:
3	chr12:50259278..50261065-chr12:50464788..50467159,2	K562	blood:
4	chr12:50260640..50261252-chr12:50432739..50433258,2	MCF-7	breast:
5	chr12:50260757..50261520-chr12:50360476..50361400,3	K562	blood:
6	chr12:50176059..50178005-chr12:50259568..50261964,2	K562	blood:
7	chr12:50259475..50261235-chr12:50302095..50303974,2	MCF-7	breast:
8	chr12:50260274..50261533-chr12:50360450..50361889,7	MCF-7	breast:
9	chr12:50259914..50262482-chr12:50360681..50362364,3	K562	blood:
10	chr12:50260625..50261504-chr12:50367677..50368552,3	MCF-7	breast:
11	chr12:50260815..50261690-chr12:50339307..50339942,3	MCF-7	breast:
12	chr12:50260640..50261184-chr12:50332011..50333010,2	MCF-7	breast:
13	chr12:50260668..50261552-chr12:50339046..50340247,7	MCF-7	breast:
14	chr12:50259734..50262522-chr12:50450953..50452874,2	MCF-7	breast:
15	chr12:50260695..50261429-chr12:50456512..50457389,2	MCF-7	breast:
16	chr12:50260690..50261529-chr12:50464081..50464704,4	MCF-7	breast:
17	chr12:50260411..50261384-chr12:50449745..50450389,4	MCF-7	breast:
18	chr12:50260529..50262269-chr12:50360474..50361834,19	MCF-7	breast:
19	chr12:50170241..50170763-chr12:50260581..50261431,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000086159	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10747567	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10747568	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783321	0.83[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783323	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783326	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875984	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875986	0.82[EUR][1000 genomes]
rs11169167	0.86[JPT][hapmap]
rs1563168	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1869504	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1965873	0.91[EUR][1000 genomes]
rs1975732	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271687	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271688	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3741557	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3741558	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4391887	0.80[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs4898512	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4898513	0.91[EUR][1000 genomes]
rs4898536	0.83[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4898537	0.83[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4898539	0.83[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67723963	0.91[EUR][1000 genomes]
rs706797	0.80[EUR][1000 genomes]
rs706798	0.86[TSI][hapmap]
rs7133995	0.89[ASN][1000 genomes]
rs7137210	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7295882	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302465	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7306374	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7307673	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7310206	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7954572	0.83[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967564	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969178	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs836967	0.91[TSI][hapmap]
rs897057	0.91[TSI][hapmap]
rs9805137	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh 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 target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1044677	C12orf62	cis	parietal	SCAN
rs1044677	RAPGEF3	cis	parietal	SCAN
rs1044677	TMBIM6	cis	cerebellum	SCAN
rs1044677	AQP2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50237600-50261200	Weak transcription	Right Atrium	heart
2	chr12:50258000-50261200	Weak transcription	Fetal Intestine Large	intestine
3	chr12:50258400-50261000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:50258600-50261000	Weak transcription	Fetal Heart	heart
5	chr12:50260400-50261400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr12:50260600-50261400	Flanking Bivalent TSS/Enh	HepG2	liver
7	chr12:50260600-50261600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:50260600-50262600	Enhancers	K562	blood
9	chr12:50260600-50262800	Enhancers	Fetal Muscle Trunk	muscle
10	chr12:50260600-50263000	Flanking Active TSS	Hela-S3	cervix
11	chr12:50260600-50263200	Enhancers	Fetal Brain Female	brain
12	chr12:50260600-50263400	Enhancers	Brain Anterior Caudate	brain
13	chr12:50260600-50263800	Enhancers	Brain Hippocampus Middle	brain
14	chr12:50260600-50264600	Enhancers	Fetal Brain Male	brain
15	chr12:50260600-50265200	Enhancers	Right Ventricle	heart
16	chr12:50260600-50267600	Enhancers	HSMM	muscle
17	chr12:50260600-50268200	Enhancers	HSMMtube	muscle
18	chr12:50260600-50268600	Enhancers	Fetal Muscle Leg	muscle
19	chr12:50260800-50261000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:50260800-50261000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:50260800-50261000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:50260800-50261000	Enhancers	Gastric	stomach
23	chr12:50260800-50261200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr12:50260800-50261200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:50260800-50261400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr12:50260800-50261400	Enhancers	A549	lung
27	chr12:50260800-50262000	Enhancers	Esophagus	oesophagus
28	chr12:50260800-50262000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr12:50260800-50262200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:50260800-50263400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:50260800-50263600	Enhancers	Brain Angular Gyrus	brain
32	chr12:50260800-50263600	Enhancers	Brain Cingulate Gyrus	brain
33	chr12:50260800-50263600	Enhancers	Brain Substantia Nigra	brain
34	chr12:50260800-50263800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:50260800-50263800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:50260800-50263800	Enhancers	Pancreas	Pancrea
37	chr12:50260800-50263800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr12:50260800-50263800	Enhancers	Stomach Mucosa	stomach
39	chr12:50260800-50264000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:50260800-50264000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr12:50260800-50264000	Enhancers	Fetal Intestine Small	intestine

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