Variant report

Variant	rs4760685
Chromosome Location	chr12:48520969-48520970
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48520102..48522830-chr12:48525176..48527649,3	MCF-7	breast:
2	chr12:48518519..48521118-chr12:48522824..48524892,2	MCF-7	breast:
3	chr12:48518675..48521479-chr12:48527987..48530696,2	K562	blood:
4	chr12:48518431..48521304-chr12:48539772..48542684,2	K562	blood:
5	chr12:48518849..48522822-chr12:48523598..48527122,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf68-4	chr12:48518472-48521203	refGeneNc_211_NR_027499

No data

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1018973	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10492080	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1074174	0.81[JPT][hapmap]
rs10783230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783231	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs10783232	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10875751	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168451	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11168455	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs11609399	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11612578	0.95[JPT][hapmap]
rs11613485	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11613781	0.94[ASN][1000 genomes]
rs12822085	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1476608	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs1489111	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs17122565	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs17122612	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs17122651	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs1968071	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2258342	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2634699	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2732455	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2732477	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2732487	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3742074	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4075913	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4141065	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4760611	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs4760620	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4760683	0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4760692	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4760698	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs57655233	0.94[ASN][1000 genomes]
rs58331734	0.94[ASN][1000 genomes]
rs6580653	0.87[ASN][1000 genomes]
rs6580656	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs6580660	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs726354	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs72644845	0.94[ASN][1000 genomes]
rs72644846	0.93[ASN][1000 genomes]
rs7296913	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7312326	1.00[JPT][hapmap]
rs7315258	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7485057	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs7485824	0.87[ASN][1000 genomes]
rs757556	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7963934	1.00[JPT][hapmap]
rs7969749	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7971668	1.00[JPT][hapmap]
rs879242	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs901964	0.81[CHB][hapmap];0.81[JPT][hapmap]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4760685	PRPF40B	cis	parietal	SCAN
rs4760685	ASB8	cis	cerebellum	SCAN
rs4760685	PRKAG1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48513400-48524800	Weak transcription	Liver	Liver
2	chr12:48513400-48526600	Weak transcription	Spleen	Spleen
3	chr12:48513600-48526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:48513600-48527000	Weak transcription	Pancreas	Pancrea
5	chr12:48513800-48524400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:48513800-48525000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:48513800-48525000	Weak transcription	Lung	lung
8	chr12:48513800-48525800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:48513800-48526000	Weak transcription	Colonic Mucosa	Colon
10	chr12:48513800-48526400	Weak transcription	Gastric	stomach
11	chr12:48513800-48526600	Weak transcription	Thymus	Thymus
12	chr12:48513800-48526800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:48514000-48521200	Weak transcription	Primary B cells from cord blood	blood
14	chr12:48514000-48522000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:48514000-48522200	Weak transcription	Adipose Nuclei	Adipose
16	chr12:48514000-48523200	Weak transcription	Fetal Kidney	kidney
17	chr12:48514000-48524200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:48514000-48524200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:48514000-48524600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr12:48514000-48525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:48514000-48525000	Weak transcription	Brain Substantia Nigra	brain
22	chr12:48514000-48525000	Weak transcription	Esophagus	oesophagus
23	chr12:48514000-48525600	Weak transcription	Placenta	Placenta
24	chr12:48514000-48526400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:48514000-48526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:48514000-48526600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:48514200-48523200	Weak transcription	HSMMtube	muscle
30	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:48514400-48523200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:48514400-48525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:48514400-48526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:48514600-48526200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:48514800-48526000	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:48515200-48523400	Weak transcription	Dnd41	blood
37	chr12:48515400-48522200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:48515800-48522000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:48515800-48522400	Strong transcription	NHDF-Ad	bronchial
41	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:48516200-48529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:48516400-48521400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:48516400-48522200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:48516400-48523000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:48516400-48524200	Strong transcription	HMEC	breast
50	chr12:48516400-48529400	Strong transcription	Ovary	ovary

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