Variant report

Variant	rs2252634
Chromosome Location	chr11:120415823-120415824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11217913	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278730	0.86[EUR][1000 genomes]
rs12278740	0.87[EUR][1000 genomes]
rs2252494	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253023	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2266100	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2266101	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2266132	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2266134	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2510876	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2510877	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4936519	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61900898	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1051115	chr11:120376808-120446434	Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1036388	chr11:120395104-120427135	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1054301	chr11:120396485-120465800	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1053749	chr11:120398643-120417586	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1035499	chr11:120398643-120446434	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1049494	chr11:120400115-120453381	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1052932	chr11:120406628-120442955	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2252634	PVRL1	cis	parietal	SCAN
rs2252634	TTC36	cis	parietal	SCAN
rs2252634	DPAGT1	cis	cerebellum	SCAN
rs2252634	C1QTNF5	cis	parietal	SCAN
rs2252634	TREH	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120398600-120417200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:120403800-120417000	Weak transcription	Right Atrium	heart
3	chr11:120403800-120418800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:120403800-120418800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:120411000-120416800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:120411800-120416800	Weak transcription	NH-A	brain
7	chr11:120411800-120417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:120412000-120416400	Weak transcription	Ovary	ovary
9	chr11:120412000-120416600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:120412200-120416600	Weak transcription	HSMM	muscle
11	chr11:120412200-120416600	Weak transcription	NHLF	lung
12	chr11:120412400-120416600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:120412400-120416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:120412400-120416800	Weak transcription	Placenta	Placenta
15	chr11:120412400-120418600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:120412600-120417800	Weak transcription	Fetal Intestine Large	intestine
17	chr11:120412600-120417800	Weak transcription	Fetal Intestine Small	intestine
18	chr11:120413800-120417600	Enhancers	HSMMtube	muscle
19	chr11:120414600-120419200	Enhancers	Primary B cells from peripheral blood	blood
20	chr11:120415400-120419200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:120415600-120416000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr11:120415600-120417000	Weak transcription	Fetal Heart	heart
23	chr11:120415600-120417600	Enhancers	Primary B cells from cord blood	blood
24	chr11:120415800-120416000	Enhancers	Fetal Muscle Trunk	muscle
25	chr11:120415800-120417200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:120415800-120420800	Enhancers	Fetal Lung	lung

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