Variant report

Variant	rs10878616
Chromosome Location	chr12:67834137-67834138
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	chr12:67827399..67830001-chr12:67831925..67834912,2	MCF-7	breast:
2	chr12:67831385..67834151-chr12:68041214..68044074,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127334	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10506549	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11176738	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176739	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176744	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12828359	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882033	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs1882280	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882282	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882283	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870937	0.82[JPT][hapmap]
rs35583684	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4913247	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913248	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913249	0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913323	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4913324	0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67939426	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132295	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132301	0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298082	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312115	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312371	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7312608	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958866	0.85[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1054111	chr12:67556780-67865542	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10878616	CAND1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67825400-67835200	Weak transcription	Ovary	ovary
2	chr12:67825600-67835400	Weak transcription	Fetal Kidney	kidney
3	chr12:67826600-67835200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:67827800-67835400	Weak transcription	NHEK	skin
5	chr12:67829000-67835400	Weak transcription	Liver	Liver
6	chr12:67829200-67835200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:67829200-67835400	Weak transcription	Fetal Lung	lung
8	chr12:67829400-67835400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:67830000-67835200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:67830000-67835600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:67830000-67835600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:67830000-67836000	Weak transcription	Psoas Muscle	Psoas
13	chr12:67830200-67835200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:67830200-67835200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:67830200-67835200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:67830400-67835200	Weak transcription	NHDF-Ad	bronchial
17	chr12:67830600-67835200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:67830600-67835200	Weak transcription	Fetal Intestine Small	intestine
19	chr12:67830600-67835200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:67830600-67835400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:67830800-67835400	Weak transcription	NH-A	brain
22	chr12:67831000-67835000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:67831000-67835000	Weak transcription	Stomach Mucosa	stomach
24	chr12:67831000-67835400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:67831000-67836600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:67831200-67835200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:67831200-67835200	Weak transcription	HSMM	muscle
28	chr12:67831200-67835200	Weak transcription	NHLF	lung
29	chr12:67831200-67835400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:67831200-67835400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:67831400-67836000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:67831600-67835200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:67831800-67835000	Weak transcription	Fetal Heart	heart
34	chr12:67831800-67835200	Weak transcription	Right Atrium	heart
35	chr12:67831800-67835400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:67831800-67835600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:67832000-67835200	Weak transcription	Fetal Intestine Large	intestine
38	chr12:67834000-67835600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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