Variant report

Variant	rs7313748
Chromosome Location	chr12:122369762-122369763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122355684..122357967-chr12:122369270..122371880,2	K562	blood:
2	chr12:122353628..122357829-chr12:122368964..122373628,4	MCF-7	breast:
3	chr12:122369123..122373485-chr12:122458454..122462950,5	K562	blood:
4	chr12:122367527..122369805-chr12:122380881..122383741,2	K562	blood:
5	chr12:122367337..122370180-chr12:122371925..122374868,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction
ENSG00000110987	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1168658	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1168661	0.80[EUR][1000 genomes]
rs1169076	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1169081	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1169083	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1169084	0.86[ASW][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[ASN][1000 genomes]
rs1169086	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1169091	0.86[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs1177588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1179947	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1184893	0.91[ASN][1000 genomes]
rs12578258	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579389	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579730	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1375653	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1375654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1375655	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs14259	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1630699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1667586	0.99[ASN][1000 genomes]
rs1678952	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs1678953	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1720030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1720066	0.81[EUR][1000 genomes]
rs1720068	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17852561	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814592	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2009257	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2272133	0.87[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs2272135	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2309275	0.95[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2442439	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688409	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688411	0.95[ASN][1000 genomes]
rs2922797	0.95[ASN][1000 genomes]
rs2948663	0.95[ASN][1000 genomes]
rs2948664	0.94[ASN][1000 genomes]
rs35252940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825172	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs4069666	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs482421	0.81[EUR][1000 genomes]
rs483416	1.00[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs508395	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs529736	0.86[ASN][1000 genomes]
rs55826938	0.81[EUR][1000 genomes]
rs56177852	0.81[EUR][1000 genomes]
rs58379261	0.81[EUR][1000 genomes]
rs59517025	0.81[EUR][1000 genomes]
rs59972569	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686220	0.99[ASN][1000 genomes]
rs7309105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap]
rs745327	0.82[CHB][hapmap]
rs830115	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs830121	0.86[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs876934	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7313748	SUDS3	cis	cerebellum	SCAN
rs7313748	WDR66	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122357000-122370200	Weak transcription	Brain Anterior Caudate	brain
2	chr12:122357000-122370600	Weak transcription	Aorta	Aorta
3	chr12:122357000-122380400	Weak transcription	Gastric	stomach
4	chr12:122357000-122383600	Weak transcription	Primary T cells from cord blood	blood
5	chr12:122363000-122384800	Weak transcription	Psoas Muscle	Psoas
6	chr12:122363000-122393400	Weak transcription	Brain Angular Gyrus	brain
7	chr12:122363200-122384600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:122363400-122372000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:122363400-122375000	Weak transcription	Spleen	Spleen
10	chr12:122363400-122377000	Weak transcription	Fetal Intestine Small	intestine
11	chr12:122363600-122369800	Weak transcription	Fetal Kidney	kidney
12	chr12:122363600-122370400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:122363600-122371600	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:122363600-122374400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:122363600-122374400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:122363600-122374600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:122363600-122375000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:122363600-122375000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:122363600-122375400	Weak transcription	Right Atrium	heart
20	chr12:122363600-122377400	Weak transcription	Fetal Brain Female	brain
21	chr12:122363600-122383600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:122363600-122383800	Weak transcription	Fetal Brain Male	brain
23	chr12:122363600-122385600	Weak transcription	Fetal Lung	lung
24	chr12:122363600-122392200	Weak transcription	Left Ventricle	heart
25	chr12:122363600-122398600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
27	chr12:122363800-122371000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:122364400-122372000	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:122365400-122375000	Weak transcription	Lung	lung
30	chr12:122365600-122370600	Weak transcription	Pancreas	Pancrea
31	chr12:122365600-122385800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:122365600-122393400	Weak transcription	Brain Substantia Nigra	brain
33	chr12:122365800-122370600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:122365800-122371200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:122365800-122371200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:122365800-122371200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:122365800-122371600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:122365800-122374600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:122365800-122375000	Weak transcription	Liver	Liver
40	chr12:122365800-122390200	Weak transcription	HUVEC	blood vessel
41	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:122366000-122370600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:122366000-122370800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:122366000-122371000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:122366000-122371000	Weak transcription	A549	lung
46	chr12:122366000-122371200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:122366000-122371200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:122366000-122371200	Weak transcription	Fetal Thymus	thymus
49	chr12:122366000-122371400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:122366000-122371400	Weak transcription	NH-A	brain

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