Variant report

Variant	rs7999270
Chromosome Location	chr13:48701059-48701060
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48699791..48701877-chr13:48806466..48810071,5	MCF-7	breast:
2	chr13:48700736..48702519-chr13:48877364..48879674,2	MCF-7	breast:
3	chr13:48700764..48701721-chr13:49342977..49343886,4	K562	blood:
4	chr13:48700823..48701797-chr13:48806881..48808213,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136156	Chromatin interaction
ENSG00000231473	Chromatin interaction
ENSG00000139687	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12869161	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12874522	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1326133	0.89[EUR][1000 genomes]
rs1326137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1327656	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1359616	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1410116	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1752129	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1886977	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1927214	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1998988	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1998989	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025864	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2094190	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2094193	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2094195	0.85[EUR][1000 genomes]
rs2094196	1.00[JPT][hapmap]
rs2148939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148940	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2182373	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2182378	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2182785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406694	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406796	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406798	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2765077	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3862747	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3990876	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4427704	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4941618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs4941620	0.85[EUR][1000 genomes]
rs4941624	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4942720	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4942721	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4942723	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4942724	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4942732	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4942734	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4942736	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4942740	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4942746	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61973264	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61973265	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61973266	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61973307	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61973308	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61974562	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61974563	0.89[EUR][1000 genomes]
rs61974564	0.89[EUR][1000 genomes]
rs61974579	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6561414	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6561416	0.89[EUR][1000 genomes]
rs6561421	0.89[EUR][1000 genomes]
rs6561425	0.89[EUR][1000 genomes]
rs6561426	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6561438	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7317685	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323702	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7323821	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7324368	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7325175	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7326381	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7326418	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7329137	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7329266	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7329615	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7332363	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7332994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7335797	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7336170	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73481288	0.96[ASN][1000 genomes]
rs73483108	0.96[ASN][1000 genomes]
rs73483122	0.96[ASN][1000 genomes]
rs7985469	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7990099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7990541	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7991892	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7996051	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7996581	0.85[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7998786	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001032	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001509	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8002482	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8002847	0.83[EUR][1000 genomes]
rs840428	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs840429	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs840432	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs840435	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs840437	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs840439	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9316350	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9316351	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs943066	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs943067	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9526419	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9526431	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9526441	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9526448	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9526450	1.00[ASN][1000 genomes]
rs9526454	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534884	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9534934	1.00[CEU][hapmap]
rs9534956	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9534959	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562792	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9567988	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[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	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7999270	MED4	cis	lesional skin	skin_eQTL
rs7999270	MED4	cis	uninvolved skin	skin_eQTL
rs7999270	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs7999270	MED4	cis	multi-tissue	Pritchard
rs7999270	MED4	cis	normal skin	skin_eQTL
rs7999270	SUCLA2	cis	multi-tissue	Pritchard

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48695800-48701200	Weak transcription	Fetal Intestine Small	intestine
2	chr13:48696200-48701200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:48696200-48701200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr13:48697400-48701400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr13:48697800-48702200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr13:48698600-48701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:48698600-48701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:48698600-48701400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr13:48698600-48701400	Weak transcription	Small Intestine	intestine
10	chr13:48698800-48701200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:48698800-48701200	Weak transcription	NHEK	skin
12	chr13:48698800-48701400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr13:48699600-48701200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:48699600-48702000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:48699600-48702200	Enhancers	Rectal Smooth Muscle	rectum
16	chr13:48699800-48701600	Enhancers	Brain Hippocampus Middle	brain
17	chr13:48699800-48701600	Enhancers	Fetal Lung	lung
18	chr13:48699800-48701800	Enhancers	Fetal Kidney	kidney
19	chr13:48700000-48701200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:48700000-48701200	Weak transcription	Placenta	Placenta
21	chr13:48700000-48702000	Enhancers	Liver	Liver
22	chr13:48700200-48701200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:48700200-48701200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr13:48700200-48701200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr13:48700200-48701200	Weak transcription	Right Atrium	heart
26	chr13:48700200-48701400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:48700200-48701600	Weak transcription	Ovary	ovary
28	chr13:48700400-48701200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:48700400-48701200	Enhancers	Stomach Smooth Muscle	stomach
30	chr13:48700400-48701200	Enhancers	HepG2	liver
31	chr13:48700400-48701400	Enhancers	Adipose Nuclei	Adipose
32	chr13:48700400-48701400	Weak transcription	Aorta	Aorta
33	chr13:48700400-48701400	Weak transcription	Right Ventricle	heart
34	chr13:48700400-48701400	Weak transcription	HSMMtube	muscle
35	chr13:48700400-48701400	Enhancers	HUVEC	blood vessel
36	chr13:48700400-48701600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr13:48700400-48702200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:48700400-48702200	Enhancers	Colon Smooth Muscle	Colon
39	chr13:48700400-48705600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr13:48700600-48701600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:48700600-48702000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr13:48701000-48701200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr13:48701000-48701200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr13:48701000-48701200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr13:48701000-48701200	Enhancers	Brain Anterior Caudate	brain
46	chr13:48701000-48701200	Enhancers	Dnd41	blood
47	chr13:48701000-48701400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr13:48701000-48701600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr13:48701000-48701600	Enhancers	Osteobl	bone
50	chr13:48701000-48701800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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