Variant report

Variant	rs12768746
Chromosome Location	chr10:1087551-1087552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:1086551..1092852-chr10:1093358..1097808,14	MCF-7	breast:
2	chr10:1082960..1085323-chr10:1085566..1087572,2	MCF-7	breast:
3	chr10:976152..979108-chr10:1085303..1088696,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047056	Chromatin interaction
ENSG00000067064	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000229869	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10159718	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10794718	0.95[JPT][hapmap]
rs10903362	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10903366	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10903367	0.88[CEU][hapmap]
rs10903370	0.86[JPT][hapmap]
rs10903371	0.80[JPT][hapmap]
rs11250256	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11250260	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[JPT][hapmap]
rs12569676	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12777134	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12782861	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12784270	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1871626	0.80[JPT][hapmap]
rs2101050	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2127608	0.81[CEU][hapmap]
rs2242271	0.81[CHB][hapmap]
rs2472533	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35405102	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3750729	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3793774	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[JPT][hapmap]
rs3793777	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3816735	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs3829165	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4519019	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4880757	0.86[CHB][hapmap]
rs4880765	0.86[JPT][hapmap]
rs4880766	0.90[JPT][hapmap]
rs5014941	0.80[JPT][hapmap]
rs56289911	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7074721	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7079726	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7082272	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7087381	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7099607	0.86[CHB][hapmap]
rs7923347	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking 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 target site	34 gene(s)	inside rSNPs	diseases
9	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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	30 gene(s)	inside rSNPs	diseases
15	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
17	nsv1040178	chr10:1024910-1126104	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv540410	chr10:1024910-1126104	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv894722	chr10:1058837-1274538	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
20	nsv1046220	chr10:1064024-1188998	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
21	nsv894723	chr10:1073684-1259485	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
22	nsv5532	chr10:1079499-1101700	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
23	nsv894724	chr10:1084942-1116294	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12768746	IDI1	cis	cerebellum	SCAN
rs12768746	C10orf110	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1035000-1094000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:1060000-1091600	Weak transcription	Hela-S3	cervix
3	chr10:1063200-1092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:1063600-1088200	Weak transcription	Fetal Brain Male	brain
5	chr10:1064000-1088400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:1065800-1087800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:1066600-1088200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:1067400-1089400	Weak transcription	Pancreas	Pancrea
9	chr10:1073400-1091800	Weak transcription	Fetal Heart	heart
10	chr10:1079800-1087800	Weak transcription	Ovary	ovary
11	chr10:1081600-1089600	Weak transcription	Psoas Muscle	Psoas
12	chr10:1081800-1089200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:1082000-1089800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr10:1082400-1088800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:1082400-1089000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:1082400-1089800	Strong transcription	Brain Germinal Matrix	brain
17	chr10:1082400-1090200	Strong transcription	Fetal Intestine Large	intestine
18	chr10:1082600-1089400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:1082600-1089400	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr10:1082600-1089600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr10:1082600-1089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:1082600-1090000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr10:1082600-1094000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr10:1082800-1087600	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr10:1082800-1088600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr10:1082800-1088800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr10:1082800-1089000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:1082800-1089000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr10:1082800-1089400	Weak transcription	Gastric	stomach
30	chr10:1082800-1089600	Weak transcription	Right Atrium	heart
31	chr10:1082800-1090200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:1083000-1088000	Strong transcription	Adipose Nuclei	Adipose
33	chr10:1083000-1088600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr10:1083000-1088600	Strong transcription	Dnd41	blood
35	chr10:1083000-1089400	Weak transcription	Esophagus	oesophagus
36	chr10:1083000-1089400	Strong transcription	Fetal Thymus	thymus
37	chr10:1083000-1090000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:1083000-1090400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:1083200-1088400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr10:1083200-1089000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr10:1083200-1089200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:1083200-1089200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr10:1083200-1089200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr10:1083200-1090400	Strong transcription	NH-A	brain
45	chr10:1083400-1089200	Strong transcription	Liver	Liver
46	chr10:1083400-1089800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:1083400-1090000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:1083400-1092000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:1083600-1087600	Strong transcription	Brain Hippocampus Middle	brain
50	chr10:1083600-1089000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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