Variant report

Variant	rs6488505
Chromosome Location	chr12:12313511-12313512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11054765	1.00[JPT][hapmap]
rs11834619	0.80[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488506	1.00[CHB][hapmap]
rs7310632	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs7310718	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7310868	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315313	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963810	1.00[CHB][hapmap]
rs7971789	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7972682	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7980348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6488505	GBP6	trans	lymphoblastoid	seeQTL
rs6488505	CLIC2	trans	lymphoblastoid	seeQTL
rs6488505	FAM171A1	trans	lymphoblastoid	seeQTL
rs6488505	CADM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
3	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
5	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
7	chr12:12279800-12313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
10	chr12:12285600-12315000	Weak transcription	Fetal Heart	heart
11	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:12288200-12342800	Weak transcription	K562	blood
13	chr12:12289400-12318200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:12297200-12318000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:12297600-12321400	Weak transcription	Gastric	stomach
16	chr12:12300600-12315800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:12302000-12318000	Weak transcription	Stomach Mucosa	stomach
18	chr12:12302200-12325000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:12302800-12317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:12303600-12318200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:12303800-12316200	Weak transcription	GM12878-XiMat	blood
23	chr12:12303800-12316600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:12303800-12335600	Weak transcription	Right Ventricle	heart
25	chr12:12304000-12315000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:12304000-12315000	Weak transcription	Brain Substantia Nigra	brain
27	chr12:12304000-12319800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:12304200-12313600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:12305400-12317400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:12305400-12318000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:12305800-12313600	Strong transcription	Liver	Liver
33	chr12:12306600-12315400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:12306600-12318200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:12306800-12325200	Weak transcription	Small Intestine	intestine
36	chr12:12307800-12317600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:12308600-12315800	Strong transcription	HepG2	liver
38	chr12:12309600-12318000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:12310000-12314800	Weak transcription	Placenta	Placenta
40	chr12:12310000-12321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:12310200-12314200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:12310800-12314000	Strong transcription	Fetal Kidney	kidney
43	chr12:12311200-12317400	Weak transcription	Fetal Brain Male	brain
44	chr12:12311800-12314200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr12:12312000-12313800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:12312000-12317400	Weak transcription	Brain Angular Gyrus	brain
47	chr12:12312000-12317400	Weak transcription	Brain Anterior Caudate	brain
48	chr12:12312000-12317400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:12312000-12325000	Weak transcription	Aorta	Aorta
50	chr12:12312000-12325000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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