Variant report

Variant	rs7946331
Chromosome Location	chr11:18400973-18400974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18400049..18401686-chr11:18404314..18405882,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10766473	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766475	0.85[JPT][hapmap]
rs10766476	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832926	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10832927	0.90[JPT][hapmap]
rs11024636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1830425	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1830426	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs1881716	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2403278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2403279	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2403280	0.85[AMR][1000 genomes]
rs2403298	0.81[AMR][1000 genomes]
rs3758680	0.86[JPT][hapmap]
rs3758681	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758682	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs3758683	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3781641	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs3809096	0.84[JPT][hapmap]
rs4274186	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs6486422	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6486423	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6486424	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6486425	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7106099	0.86[JPT][hapmap]
rs7111748	0.89[JPT][hapmap]
rs7112492	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7121244	0.86[JPT][hapmap]
rs7128549	0.86[JPT][hapmap]
rs7129689	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7925445	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7938267	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7938942	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs7943847	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv523373	chr11:18382911-18401531	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv1811183	chr11:18389643-18432437	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7946331	LDHC	cis	lymphoblastoid	seeQTL
rs7946331	LDHC	cis	cerebellum	SCAN
rs7946331	LDHAL6A	cis	parietal	SCAN
rs7946331	LDHA	cis	cerebellum	SCAN
rs7946331	LDHAL6A	cis	cerebellum	SCAN
rs7946331	RRAS2	cis	cerebellum	SCAN
rs7946331	LDHC	cis	parietal	SCAN
rs7946331	C11orf58	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:18387600-18404200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:18387600-18404400	Weak transcription	Esophagus	oesophagus
4	chr11:18387600-18404800	Weak transcription	Pancreas	Pancrea
5	chr11:18387800-18404400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:18388000-18405000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:18388400-18402600	Weak transcription	Hela-S3	cervix
8	chr11:18388800-18404400	Weak transcription	Brain Anterior Caudate	brain
9	chr11:18389200-18404600	Weak transcription	Thymus	Thymus
10	chr11:18390000-18404400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:18390000-18404400	Weak transcription	Fetal Brain Female	brain
12	chr11:18390200-18404200	Weak transcription	Fetal Thymus	thymus
13	chr11:18390400-18404000	Weak transcription	NHDF-Ad	bronchial
14	chr11:18390400-18404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:18390400-18404200	Weak transcription	HMEC	breast
16	chr11:18390400-18404600	Weak transcription	Primary B cells from cord blood	blood
17	chr11:18390400-18404800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:18390600-18404200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:18390600-18404200	Weak transcription	Adipose Nuclei	Adipose
20	chr11:18390600-18404200	Weak transcription	Osteobl	bone
21	chr11:18390800-18404200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:18391200-18404200	Weak transcription	HSMM	muscle
23	chr11:18391600-18404200	Weak transcription	A549	lung
24	chr11:18393000-18404200	Weak transcription	HSMMtube	muscle
25	chr11:18393000-18404400	Weak transcription	Primary T cells from cord blood	blood
26	chr11:18393600-18404200	Weak transcription	HepG2	liver
27	chr11:18399800-18401600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:18400000-18401200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:18400400-18404200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:18400400-18404200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:18400400-18404200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr11:18400400-18404400	Weak transcription	Primary monocytes fromperipheralblood	blood

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