Variant report

Variant	rs11168963
Chromosome Location	chr12:49673158-49673159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49670426..49673698-chr12:49680662..49684493,5	K562	blood:
2	chr12:49448441..49451741-chr12:49671827..49675031,3	K562	blood:
3	chr12:49671647..49673485-chr12:49739291..49741377,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1QL4-3	chr12:49672836-49674483	ENSG00000250773
2	lnc-C1QL4-3	chr12:49672836-49674498	ENSG00000257960

Variant related genes	Relation type
ENSG00000178401	Chromatin interaction
ENSG00000167548	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10875943	0.87[CEU][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168962	1.00[ASW][hapmap];0.83[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56222401	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6580706	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs7975527	0.98[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11168963	ANO6	cis	parietal	SCAN
rs11168963	MCRS1	cis	cerebellum	SCAN
rs11168963	TMEM117	cis	cerebellum	SCAN
rs11168963	OR10AD1	cis	parietal	SCAN
rs11168963	DDN	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
2	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:49662800-49673400	Weak transcription	Brain Anterior Caudate	brain
4	chr12:49662800-49673400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:49662800-49673400	Weak transcription	Brain Substantia Nigra	brain
6	chr12:49665200-49673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:49665400-49673800	Weak transcription	Fetal Kidney	kidney
8	chr12:49665600-49673400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:49665600-49673400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:49666000-49673400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:49667200-49673200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:49667400-49673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:49667400-49673400	Weak transcription	Pancreas	Pancrea
14	chr12:49667600-49673400	Weak transcription	Left Ventricle	heart
15	chr12:49667600-49673600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:49667800-49673200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:49667800-49673200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:49667800-49673200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:49667800-49673400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:49667800-49673400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:49667800-49673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:49667800-49673400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:49667800-49673400	Weak transcription	Esophagus	oesophagus
24	chr12:49667800-49673400	Weak transcription	Fetal Intestine Large	intestine
25	chr12:49668000-49673400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:49668000-49673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:49668000-49673400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:49668000-49673400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:49668000-49673400	Weak transcription	Fetal Brain Female	brain
30	chr12:49668000-49673600	Weak transcription	Fetal Lung	lung
31	chr12:49668000-49673800	Weak transcription	Adipose Nuclei	Adipose
32	chr12:49668000-49676000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:49668000-49676000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:49668000-49678000	Weak transcription	Brain Germinal Matrix	brain
35	chr12:49668200-49673400	Weak transcription	Lung	lung
36	chr12:49668400-49673200	Weak transcription	Gastric	stomach
37	chr12:49668400-49673400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:49668400-49673400	Weak transcription	NH-A	brain
39	chr12:49668400-49673800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:49668400-49673800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:49668400-49676200	Weak transcription	NHLF	lung
42	chr12:49668600-49673200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:49668600-49673400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr12:49668600-49673400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr12:49668600-49676000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:49668600-49682400	Weak transcription	HMEC	breast
47	chr12:49668800-49673400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:49668800-49675200	Weak transcription	Spleen	Spleen
49	chr12:49669000-49673400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:49669000-49673400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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