Variant report

Variant	rs4767439
Chromosome Location	chr12:117148549-117148550
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:2)
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	chr12:117146942..117149806-chr12:117158509..117160408,2	K562	blood:
2	chr12:117147973..117150592-chr12:117175280..117177102,2	MCF-7	breast:
3	chr12:117145990..117148550-chr12:117156531..117158222,2	K562	blood:
4	chr12:116827495..116829814-chr12:117147036..117149780,2	MCF-7	breast:
5	chr12:117140715..117144764-chr12:117146137..117149297,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNFT2-1	chr12:117147983-117149097	ENSG00000250553
2	lnc-C12orf49-3	chr12:117147979-117149093	NONHSAT030961

No data

Variant related genes	Relation type
ENSG00000111412	Chromatin interaction
ENSG00000135119	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10507273	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11068156	0.94[CEU][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs11068157	0.89[ASW][hapmap];0.94[CEU][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes]
rs11068158	1.00[CEU][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs11068160	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068161	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12367425	0.83[CEU][hapmap]
rs12819414	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1566017	0.83[EUR][1000 genomes]
rs182889	0.82[ASN][1000 genomes]
rs2029852	0.86[CHB][hapmap]
rs339457	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs339460	0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4767440	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7314462	0.81[ASN][1000 genomes]
rs756120	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4767439	MED13L	cis	parietal	SCAN
rs4767439	SLC24A6	cis	cerebellum	SCAN
rs4767439	RNFT2	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117141600-117150000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:117144800-117148800	Enhancers	Fetal Thymus	thymus
3	chr12:117144800-117149000	Enhancers	Thymus	Thymus
4	chr12:117146200-117149000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:117146200-117152000	Weak transcription	Spleen	Spleen
6	chr12:117146400-117148600	Flanking Active TSS	Fetal Brain Female	brain
7	chr12:117146400-117149000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:117147000-117148800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:117147000-117150000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:117147200-117148600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:117147200-117148800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr12:117147200-117148800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:117147200-117150200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:117147200-117153000	Weak transcription	Left Ventricle	heart
15	chr12:117147200-117153000	Weak transcription	HepG2	liver
16	chr12:117147200-117153400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:117147200-117153800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:117147200-117155200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:117147200-117155400	Weak transcription	Right Atrium	heart
20	chr12:117147200-117155800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr12:117147200-117155800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:117147200-117156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:117147200-117174000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:117147400-117149000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr12:117147400-117149400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:117147400-117149600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:117147400-117150000	Weak transcription	Lung	lung
28	chr12:117147400-117150000	Weak transcription	HMEC	breast
29	chr12:117147400-117150200	Weak transcription	Gastric	stomach
30	chr12:117147400-117150200	Weak transcription	GM12878-XiMat	blood
31	chr12:117147400-117151000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:117147400-117151600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:117147400-117151800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr12:117147400-117151800	Weak transcription	Pancreas	Pancrea
35	chr12:117147400-117152000	Weak transcription	Dnd41	blood
36	chr12:117147400-117152800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:117147400-117153000	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:117147400-117153200	Weak transcription	Primary B cells from cord blood	blood
39	chr12:117147400-117153200	Weak transcription	Aorta	Aorta
40	chr12:117147400-117153400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:117147400-117153400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:117147400-117153400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:117147400-117153800	Weak transcription	Ovary	ovary
44	chr12:117147400-117154200	Weak transcription	Colonic Mucosa	Colon
45	chr12:117147400-117155400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:117147400-117155800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:117147400-117156000	Weak transcription	Colon Smooth Muscle	Colon
48	chr12:117147400-117156000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr12:117147400-117157000	Weak transcription	Right Ventricle	heart
50	chr12:117147400-117158000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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