Variant report

Variant	rs2408718
Chromosome Location	chr12:47600432-47600433
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	chr12:47598802..47603269-chr12:47603355..47607825,7	K562	blood:
2	chr12:47598762..47601784-chr12:47665654..47668413,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMIGO2-1	chr12:47599682-47601754	NONHSAT027901

Variant related genes	Relation type
ENSG00000247774	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10881077	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10881079	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183779	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs11183783	1.00[CHB][hapmap]
rs11183795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11183796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11183799	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12370192	0.84[ASW][hapmap]
rs12370622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554693	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17222290	0.84[ASW][hapmap]
rs17821774	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17822189	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1917657	0.84[ASW][hapmap]
rs2004683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2004684	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2111903	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768142	0.84[ASW][hapmap]
rs4768144	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768782	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55711758	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55849521	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712100	1.00[CHB][hapmap]
rs73110240	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs732523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7974410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs855146	1.00[CHB][hapmap]
rs855147	1.00[CHB][hapmap]
rs873935	1.00[CHB][hapmap]
rs952967	0.84[ASW][hapmap]

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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2408718	C12orf68	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47583200-47628600	Weak transcription	Aorta	Aorta
2	chr12:47584000-47600600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:47584800-47605800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:47585800-47601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:47597600-47600600	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr12:47597600-47600600	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr12:47598200-47600600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
8	chr12:47598400-47600800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr12:47598800-47601600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:47598800-47605000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:47599000-47603400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:47599200-47600600	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:47599200-47600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:47599200-47601400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:47599200-47601400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr12:47599400-47600600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:47599400-47601200	Enhancers	A549	lung
18	chr12:47599400-47601400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr12:47599600-47600600	Enhancers	Dnd41	blood
20	chr12:47599600-47601400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr12:47599600-47602600	Enhancers	Fetal Thymus	thymus
22	chr12:47599600-47605000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
23	chr12:47599800-47600800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:47599800-47601200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
25	chr12:47599800-47601400	Enhancers	Spleen	Spleen
26	chr12:47599800-47602800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:47599800-47603200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:47600000-47600600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:47600000-47601000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:47600000-47601000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:47600000-47602000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
32	chr12:47600000-47602200	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr12:47600000-47602600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr12:47600000-47606200	Weak transcription	Adipose Nuclei	Adipose
35	chr12:47600000-47614600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:47600200-47600600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr12:47600200-47600600	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr12:47600200-47601000	Flanking Active TSS	K562	blood
39	chr12:47600200-47601400	Enhancers	Small Intestine	intestine
40	chr12:47600200-47602200	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr12:47600200-47602200	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
42	chr12:47600200-47602200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:47600400-47600600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:47600400-47600600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:47600400-47600600	Enhancers	Placenta	Placenta
46	chr12:47600400-47600600	Enhancers	GM12878-XiMat	blood
47	chr12:47600400-47600600	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr12:47600400-47600800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:47600400-47602000	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
50	chr12:47600400-47602200	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood

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