Variant report

Variant	rs4757669
Chromosome Location	chr11:18523263-18523264
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	chr11:18523134..18525555-chr11:18546904..18549561,3	K562	blood:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10832939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11024691	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024709	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11024718	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11600246	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603992	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11606375	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223260	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12225251	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12226584	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16935482	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16935538	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16935539	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088184	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305167	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3802965	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3802966	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4390325	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417245	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4636650	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756948	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4756951	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4757671	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4757672	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56104322	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56138729	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56991251	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486431	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486435	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72876754	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72876774	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7483340	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928508	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7942733	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4757669	LDHC	cis	Artery Tibial	GTEx
rs4757669	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs4757669	LDHC	cis	lung	GTEx
rs4757669	LDHC	cis	Whole Blood	GTEx
rs4757669	LDHC	cis	Adipose Subcutaneous	GTEx
rs4757669	LDHC	cis	Nerve Tibial	GTEx
rs4757669	LDHC	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18483600-18526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:18496200-18538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:18504000-18540600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr11:18504600-18523400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:18504600-18523400	Weak transcription	Small Intestine	intestine
11	chr11:18504600-18523600	Weak transcription	HMEC	breast
12	chr11:18505200-18531800	Weak transcription	Fetal Brain Male	brain
13	chr11:18509000-18537600	Strong transcription	Liver	Liver
14	chr11:18509000-18540200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:18509000-18540600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:18509600-18540200	Strong transcription	Placenta	Placenta
17	chr11:18510800-18524400	Strong transcription	Dnd41	blood
18	chr11:18510800-18541400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr11:18511000-18524400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:18511800-18527000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:18512800-18523400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:18512800-18526800	Weak transcription	Spleen	Spleen
23	chr11:18513000-18526800	Weak transcription	Pancreas	Pancrea
24	chr11:18513000-18544000	Weak transcription	Gastric	stomach
25	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
26	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:18513200-18525400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:18513200-18532600	Weak transcription	Esophagus	oesophagus
29	chr11:18514600-18540800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:18514800-18539800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:18515000-18537600	Strong transcription	Fetal Thymus	thymus
32	chr11:18515000-18540000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:18515000-18540600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:18515200-18538000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
36	chr11:18515600-18537600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr11:18515600-18537800	Strong transcription	Fetal Intestine Large	intestine
38	chr11:18516200-18524400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:18516200-18524600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:18516200-18524600	Strong transcription	Fetal Brain Female	brain
41	chr11:18516200-18538200	Strong transcription	Adipose Nuclei	Adipose
42	chr11:18516200-18538800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr11:18516200-18540400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:18516400-18523400	Weak transcription	Colonic Mucosa	Colon
45	chr11:18516400-18531400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:18516400-18532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:18516400-18540400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:18516800-18541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:18517000-18524400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:18517000-18524400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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