Variant report

Variant	rs11168422
Chromosome Location	chr12:48519505-48519506
allele	G/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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48518519..48521118-chr12:48522824..48524892,2	MCF-7	breast:
2	chr12:48498208..48500662-chr12:48518314..48520006,2	K562	blood:
3	chr12:48503405..48506326-chr12:48517186..48520007,2	K562	blood:
4	chr12:48518675..48521479-chr12:48527987..48530696,2	K562	blood:
5	chr12:48518431..48521304-chr12:48539772..48542684,2	K562	blood:
6	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

Variant related genes	Relation type
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10082861	0.96[ASN][1000 genomes]
rs10219623	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10219645	0.89[ASN][1000 genomes]
rs10875731	0.80[EUR][1000 genomes]
rs10875735	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10875736	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10875737	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10875738	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875740	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10875745	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875746	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875747	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875748	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875750	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875756	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875762	0.81[ASN][1000 genomes]
rs11168374	0.80[EUR][1000 genomes]
rs11168383	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168386	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168401	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168403	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11168414	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168415	0.97[ASN][1000 genomes]
rs11168416	0.97[ASN][1000 genomes]
rs11168418	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168420	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168421	0.96[ASN][1000 genomes]
rs11168425	0.95[ASN][1000 genomes]
rs11168427	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168433	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11558768	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12296244	0.80[EUR][1000 genomes]
rs12297004	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12297470	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12301339	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12304476	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12305511	0.82[EUR][1000 genomes]
rs12305647	0.82[EUR][1000 genomes]
rs12306290	0.94[ASN][1000 genomes]
rs12306451	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12310813	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12310999	0.80[EUR][1000 genomes]
rs12311774	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12311953	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12312134	0.90[ASN][1000 genomes]
rs12313300	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12313404	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12315625	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17122620	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17122666	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1859445	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2107638	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2158516	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2228500	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269933	0.97[ASN][1000 genomes]
rs2269935	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286021	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782910	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3782911	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760619	0.93[ASN][1000 genomes]
rs4760622	0.82[EUR][1000 genomes]
rs4760680	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4760681	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760684	0.97[ASN][1000 genomes]
rs4760687	0.87[ASN][1000 genomes]
rs4760689	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760690	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760695	0.80[EUR][1000 genomes]
rs58952582	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60106007	0.97[ASN][1000 genomes]
rs60761335	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61343568	0.91[ASN][1000 genomes]
rs61918774	0.80[EUR][1000 genomes]
rs61918806	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61918809	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61918810	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs725454	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73102065	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73102067	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7485355	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486424	0.87[ASN][1000 genomes]
rs8804	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs886588	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs989144	0.89[AMR][1000 genomes];0.91[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11168422	RP1-228P16.1	cis	Artery Tibial	GTEx
rs11168422	RP1-228P16.1	cis	Thyroid	GTEx
rs11168422	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11168422	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx

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	chr12:48514000-48520200	Weak transcription	Fetal Lung	lung
14	chr12:48514000-48520600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:48514000-48521200	Weak transcription	Primary B cells from cord blood	blood
16	chr12:48514000-48522000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:48514000-48522200	Weak transcription	Adipose Nuclei	Adipose
18	chr12:48514000-48523200	Weak transcription	Fetal Kidney	kidney
19	chr12:48514000-48524200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:48514000-48524200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:48514000-48524600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:48514000-48525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:48514000-48525000	Weak transcription	Brain Substantia Nigra	brain
24	chr12:48514000-48525000	Weak transcription	Esophagus	oesophagus
25	chr12:48514000-48525600	Weak transcription	Placenta	Placenta
26	chr12:48514000-48526400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:48514000-48526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:48514000-48526600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:48514200-48523200	Weak transcription	HSMMtube	muscle
32	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr12:48514400-48523200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:48514400-48525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:48514400-48526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:48514600-48519800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:48514600-48520000	Weak transcription	NHEK	skin
38	chr12:48514600-48526200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:48514800-48526000	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:48515200-48523400	Weak transcription	Dnd41	blood
41	chr12:48515400-48522200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:48515800-48522000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:48515800-48522400	Strong transcription	NHDF-Ad	bronchial
45	chr12:48515800-48535600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr12:48515800-48545600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:48516200-48529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:48516200-48545400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:48516200-48547200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:48516400-48519600	Strong transcription	Fetal Brain Female	brain

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