Variant report

Variant	rs10431062
Chromosome Location	chr11:108370117-108370118
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr11:108370071-108370146	K562	blood:	n/a	n/a
2	ELF1	chr11:108369748-108370361	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:108366826..108370827-chr11:108463038..108466989,6	MCF-7	breast:
2	chr11:108367402..108370460-chr11:108461670..108466033,4	K562	blood:
3	chr11:108351170..108356197-chr11:108366781..108370741,5	K562	blood:
4	chr11:108369586..108372372-chr11:108483049..108485816,2	K562	blood:
5	chr11:108332946..108340923-chr11:108359972..108371658,26	K562	blood:
6	chr11:108365650..108370333-chr11:108462736..108466617,7	K562	blood:
7	chr11:108333954..108342521-chr11:108361561..108373383,35	K562	blood:

No data

Variant related genes	Relation type
KDELC2	TF binding region
ENSG00000221607	Chromatin interaction
ENSG00000166323	Chromatin interaction
ENSG00000110723	Chromatin interaction
ENSG00000178202	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2846412	0.80[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7943820	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832263	chr11:108183372-108384391	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10431062	GRIA4	cis	cerebellum	SCAN
rs10431062	KDELC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108367800-108370200	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr11:108368200-108370400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr11:108368400-108370200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr11:108368400-108370200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr11:108369400-108370400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:108369400-108370400	Flanking Active TSS	Dnd41	blood
7	chr11:108369400-108370800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:108369400-108371800	Weak transcription	Fetal Heart	heart
9	chr11:108369400-108371800	Weak transcription	HSMMtube	muscle
10	chr11:108369600-108370200	Enhancers	GM12878-XiMat	blood
11	chr11:108369600-108370200	Weak transcription	NHEK	skin
12	chr11:108369600-108370400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:108369600-108370400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:108369600-108370400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:108369600-108371000	Enhancers	Placenta	Placenta
16	chr11:108369600-108371400	Weak transcription	Gastric	stomach
17	chr11:108369600-108371400	Enhancers	K562	blood
18	chr11:108369600-108371600	Weak transcription	HSMM	muscle
19	chr11:108369600-108371800	Weak transcription	Osteobl	bone
20	chr11:108369600-108372000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:108369600-108372000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:108369600-108372000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:108369600-108372200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:108369600-108379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:108369600-108380800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:108369600-108381000	Weak transcription	Liver	Liver
27	chr11:108369600-108382200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:108369600-108384000	Weak transcription	Fetal Kidney	kidney
29	chr11:108369800-108370200	Enhancers	Ovary	ovary
30	chr11:108369800-108370200	Enhancers	Stomach Smooth Muscle	stomach
31	chr11:108369800-108370600	Enhancers	Esophagus	oesophagus
32	chr11:108369800-108371200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:108369800-108371400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:108369800-108373400	Enhancers	HepG2	liver
35	chr11:108370000-108370200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:108370000-108370200	Enhancers	Right Ventricle	heart
37	chr11:108370000-108370400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:108370000-108371200	Weak transcription	Thymus	Thymus
39	chr11:108370000-108380000	Weak transcription	Rectal Mucosa Donor 31	rectum

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