Variant report

Variant	rs2403254
Chromosome Location	chr11:18325146-18325147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18319375..18321577-chr11:18324234..18326224,2	MCF-7	breast:
2	chr11:18324297..18325987-chr11:18341504..18344479,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110768	Chromatin interaction
ENSG00000110756	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1046615	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10741740	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10741743	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766467	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766471	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10832918	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10832919	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10832920	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832923	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11024606	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024614	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11024622	0.84[EUR][1000 genomes]
rs12294486	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305565	0.80[EUR][1000 genomes]
rs3802967	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4150581	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4150589	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150606	0.92[CEU][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4150628	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4150644	0.81[AMR][1000 genomes]
rs4150678	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4757638	0.92[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs60889939	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Metabolic traits	21886157	GWAS catalog
Blood metabolite levels	24816252	GWAS catalog

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2403254	GTF2H1	cis	multi-tissue	Pritchard
rs2403254	HPS5	cis	parietal	SCAN
rs2403254	PIK3C2A	cis	cerebellum	SCAN
rs2403254	LDHA	cis	parietal	SCAN
rs2403254	GTF2H1	cis	Nerve Tibial	GTEx
rs2403254	GTF2H1	cis	lung	GTEx
rs2403254	LDHAL6A	cis	cerebellum	SCAN
rs2403254	RPS4Y1	trans	lymphoblastoid	seeQTL
rs2403254	HPS5	cis	cerebellum	SCAN
rs2403254	GTF2H1	cis	parietal	SCAN
rs2403254	GTF2H1	cis	cerebellum	SCAN
rs2403254	RPL8	trans	cerebellum	SCAN
rs2403254	SAA2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18287600-18334000	Weak transcription	Right Atrium	heart
2	chr11:18297400-18328400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:18298200-18333800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:18298600-18326200	Strong transcription	Liver	Liver
5	chr11:18298800-18327600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:18298800-18331600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:18299200-18332400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:18299600-18326200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:18299600-18334200	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr11:18300000-18328600	Weak transcription	Stomach Mucosa	stomach
11	chr11:18300000-18334400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:18300200-18333600	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:18300200-18334000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:18300200-18334800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:18300200-18336000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:18300600-18331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:18300600-18332600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:18300600-18333200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:18300600-18334000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:18300800-18328400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr11:18300800-18330200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:18300800-18333000	Strong transcription	Dnd41	blood
23	chr11:18301000-18328000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:18301000-18334400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:18302200-18333000	Strong transcription	Adipose Nuclei	Adipose
26	chr11:18303000-18327000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:18303000-18334800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:18303200-18325600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr11:18303200-18334800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:18303400-18335000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr11:18304400-18332000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr11:18304600-18332000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:18305000-18331600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr11:18305200-18332000	Strong transcription	Primary B cells from cord blood	blood
35	chr11:18305600-18335000	Strong transcription	Primary T cells from cord blood	blood
36	chr11:18307400-18332400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr11:18308000-18333000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr11:18309000-18331600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr11:18310800-18334000	Weak transcription	Esophagus	oesophagus
40	chr11:18311800-18343000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:18312800-18334400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:18313000-18333000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:18314800-18330000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:18315200-18332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr11:18315600-18327200	Strong transcription	Hela-S3	cervix
46	chr11:18316200-18333800	Weak transcription	Fetal Heart	heart
47	chr11:18316800-18326000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:18316800-18332200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr11:18317000-18330000	Weak transcription	Fetal Brain Male	brain
50	chr11:18317200-18330600	Weak transcription	Lung	lung

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