Variant report

Variant	rs4767440
Chromosome Location	chr12:117153385-117153386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117152671..117155117-chr12:117156029..117158253,2	MCF-7	breast:
2	chr12:117150782..117153045-chr12:117153235..117155739,2	MCF-7	breast:
3	chr12:117151206..117153398-chr12:117162131..117164765,2	K562	blood:
4	chr12:117145528..117148245-chr12:117152693..117154607,2	K562	blood:
5	chr12:117151653..117153224-chr12:117153245..117155923,3	MCF-7	breast:
6	chr12:117153364..117155986-chr12:117156713..117160278,5	K562	blood:

Variant related genes	Relation type
ENSG00000111412	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10507273	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068156	0.94[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs11068157	0.94[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs11068158	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11068160	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11068161	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[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	0.94[ASN][1000 genomes]
rs2029852	0.82[CHB][hapmap]
rs2468375	0.90[ASN][1000 genomes]
rs339453	0.90[ASN][1000 genomes]
rs339457	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs339460	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4767439	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	0.94[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
rs4767440	MED13L	cis	parietal	SCAN
rs4767440	SLC24A6	cis	cerebellum	SCAN
rs4767440	RNFT2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117147200-117153400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:117147200-117153800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:117147200-117155200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:117147200-117155400	Weak transcription	Right Atrium	heart
5	chr12:117147200-117155800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr12:117147200-117155800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:117147200-117156400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:117147200-117174000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:117147400-117153400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:117147400-117153400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:117147400-117153400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:117147400-117153800	Weak transcription	Ovary	ovary
13	chr12:117147400-117154200	Weak transcription	Colonic Mucosa	Colon
14	chr12:117147400-117155400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:117147400-117155800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:117147400-117156000	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:117147400-117156000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:117147400-117157000	Weak transcription	Right Ventricle	heart
19	chr12:117147400-117158000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:117147400-117173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:117147800-117153600	Weak transcription	A549	lung
22	chr12:117148200-117154200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:117148400-117153400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:117148400-117153400	Weak transcription	HSMM	muscle
25	chr12:117148400-117153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:117148400-117153800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:117148400-117154400	Weak transcription	HUVEC	blood vessel
28	chr12:117148600-117154800	Weak transcription	Psoas Muscle	Psoas
29	chr12:117148600-117155400	Weak transcription	HSMMtube	muscle
30	chr12:117148600-117164200	Weak transcription	Stomach Mucosa	stomach
31	chr12:117148800-117153400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:117148800-117154200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:117149000-117153400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:117149000-117153600	Weak transcription	NH-A	brain
35	chr12:117149000-117155000	Weak transcription	Fetal Lung	lung
36	chr12:117149000-117155200	Weak transcription	Fetal Brain Male	brain
37	chr12:117149400-117154600	Strong transcription	Fetal Stomach	stomach
38	chr12:117149400-117174000	Weak transcription	K562	blood
39	chr12:117149600-117155400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:117149600-117164200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr12:117149800-117153800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr12:117150000-117155400	Strong transcription	Lung	lung
43	chr12:117150000-117162000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:117150200-117155800	Strong transcription	Gastric	stomach
45	chr12:117150400-117153600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:117150400-117153600	Weak transcription	Liver	Liver
47	chr12:117150600-117155800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:117150800-117172600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:117151000-117153400	Weak transcription	Fetal Brain Female	brain
50	chr12:117151000-117153600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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