Variant report

Variant	rs9567994
Chromosome Location	chr13:48667878-48667879
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48667865..48670263-chr13:48806295..48809101,2	MCF-7	breast:
2	chr13:48611722..48613362-chr13:48667186..48669052,2	K562	blood:
3	chr13:48667088..48669248-chr13:48807095..48809011,2	K562	blood:
4	chr13:48651976..48654376-chr13:48667767..48670618,2	K562	blood:

Variant related genes	Relation type
ENSG00000136146	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000136156	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11616639	0.87[ASN][1000 genomes]
rs1327655	0.88[AMR][1000 genomes]
rs1410117	0.94[ASN][1000 genomes]
rs1571256	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1927213	0.97[ASN][1000 genomes]
rs2094192	0.97[ASN][1000 genomes]
rs2104480	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2148246	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2148938	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2406709	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2406797	0.99[ASN][1000 genomes]
rs3809330	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs3949847	0.82[CEU][hapmap]
rs4294712	0.93[ASN][1000 genomes]
rs4369555	0.91[JPT][hapmap]
rs4941623	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4941627	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4942742	0.80[AMR][1000 genomes]
rs4942743	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4942747	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4942748	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942749	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4942750	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4942751	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4942752	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56399021	0.91[ASN][1000 genomes]
rs59829900	0.89[AMR][1000 genomes]
rs6561434	0.81[EUR][1000 genomes]
rs7317431	0.86[AMR][1000 genomes]
rs7318704	0.86[AMR][1000 genomes]
rs7322766	0.88[AMR][1000 genomes]
rs7324484	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7326363	0.98[ASN][1000 genomes]
rs7331551	0.81[AMR][1000 genomes]
rs7332326	0.87[AMR][1000 genomes]
rs7333247	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7336214	0.99[ASN][1000 genomes]
rs7338844	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7338999	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7339370	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7986400	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7990060	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8001243	0.97[ASN][1000 genomes]
rs9316348	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9316352	0.89[AMR][1000 genomes]
rs9316353	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9316354	0.89[AMR][1000 genomes]
rs9316355	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9316356	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9316357	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9316358	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9316359	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9316362	0.81[AMR][1000 genomes]
rs9526442	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9526443	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9526445	0.99[ASN][1000 genomes]
rs9526447	0.94[ASN][1000 genomes]
rs9526449	0.97[ASN][1000 genomes]
rs9526451	0.91[ASN][1000 genomes]
rs9534888	0.90[JPT][hapmap]
rs9534931	0.83[ASN][1000 genomes]
rs9534932	0.87[ASN][1000 genomes]
rs9534933	0.90[ASN][1000 genomes]
rs9534937	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9534939	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9534943	0.97[ASN][1000 genomes]
rs9534944	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9534945	0.97[ASN][1000 genomes]
rs9534946	0.92[ASN][1000 genomes]
rs9534947	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs9534948	0.92[ASN][1000 genomes]
rs9534949	0.89[ASN][1000 genomes]
rs9534950	0.99[ASN][1000 genomes]
rs9534951	0.91[ASN][1000 genomes]
rs9534952	0.93[ASN][1000 genomes]
rs9534957	0.98[ASN][1000 genomes]
rs9534961	0.85[ASN][1000 genomes]
rs9534965	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs9562802	0.97[ASN][1000 genomes]
rs9562806	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9562808	0.86[AMR][1000 genomes]
rs9567987	0.95[ASN][1000 genomes]
rs9567991	0.97[ASN][1000 genomes]
rs9567999	0.81[EUR][1000 genomes]
rs9568000	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568001	0.88[AMR][1000 genomes]
rs9568002	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568003	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568004	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568005	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568006	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568008	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568009	0.86[AMR][1000 genomes]
rs9568010	0.88[AMR][1000 genomes]
rs9568014	0.84[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes]
rs9591135	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9591138	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9591139	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9595835	0.88[CEU][hapmap]
rs9595851	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	40 gene(s)	inside rSNPs	diseases
2	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9567994	MED4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48652800-48668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:48653000-48668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:48653200-48668200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:48655400-48668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:48655400-48668200	Weak transcription	Aorta	Aorta
6	chr13:48656200-48668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:48657400-48668000	Weak transcription	HSMMtube	muscle
8	chr13:48659600-48668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:48659800-48668200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr13:48662400-48668200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr13:48664600-48668200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr13:48664800-48668000	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr13:48664800-48668000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:48664800-48668000	Enhancers	Fetal Heart	heart
15	chr13:48665800-48668000	Enhancers	Liver	Liver
16	chr13:48666000-48668200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr13:48666400-48668000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr13:48666600-48668000	Enhancers	Primary B cells from cord blood	blood
19	chr13:48666600-48668000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr13:48666600-48668000	Enhancers	Small Intestine	intestine
21	chr13:48666600-48668200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr13:48666600-48668200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr13:48666600-48668400	Enhancers	Spleen	Spleen
24	chr13:48666800-48668000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:48666800-48668000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr13:48666800-48668000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr13:48666800-48668000	Enhancers	Fetal Intestine Small	intestine
28	chr13:48666800-48668000	Enhancers	Stomach Smooth Muscle	stomach
29	chr13:48666800-48668400	Enhancers	Primary B cells from peripheral blood	blood
30	chr13:48666800-48668400	Enhancers	Pancreas	Pancrea
31	chr13:48666800-48668600	Flanking Active TSS	Dnd41	blood
32	chr13:48666800-48669400	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr13:48667000-48668000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:48667000-48668000	Enhancers	Brain Anterior Caudate	brain
35	chr13:48667000-48668000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr13:48667000-48668000	Enhancers	Thymus	Thymus
37	chr13:48667000-48668400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr13:48667000-48668600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:48667000-48669400	Active TSS	K562	blood
40	chr13:48667200-48668000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:48667200-48668000	Enhancers	Fetal Muscle Leg	muscle
42	chr13:48667200-48668200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr13:48667200-48668600	Flanking Active TSS	Hela-S3	cervix
44	chr13:48667400-48668000	Enhancers	Primary T cells from cord blood	blood
45	chr13:48667400-48668000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr13:48667400-48668200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr13:48667400-48668600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr13:48667600-48668000	Enhancers	H1 Cell Line	embryonic stem cell
49	chr13:48667600-48668000	Active TSS	H9 Cell Line	embryonic stem cell
50	chr13:48667600-48668000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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