Variant report

Variant	rs224572
Chromosome Location	chr12:51416520-51416521
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
2	chr12:51404460..51409575-chr12:51416331..51420356,8	MCF-7	breast:
3	chr12:51381999..51383728-chr12:51415428..51417446,2	MCF-7	breast:
4	chr12:51416514..51419391-chr12:51663583..51665592,2	MCF-7	breast:
5	chr12:51158188..51159927-chr12:51415849..51417938,2	K562	blood:
6	chr12:51393084..51395626-chr12:51414543..51417529,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000272028	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10275	0.89[EUR][1000 genomes]
rs10783409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783410	0.82[EUR][1000 genomes]
rs10876127	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876128	0.92[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs10876129	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876130	0.88[CEU][hapmap];0.85[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876131	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876132	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876136	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs10876138	1.00[CHB][hapmap]
rs10876139	0.84[EUR][1000 genomes]
rs1095999	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169657	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169695	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169707	0.81[EUR][1000 genomes]
rs11169710	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11610644	0.80[ASN][1000 genomes]
rs12370120	0.83[EUR][1000 genomes]
rs12379	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12424509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427345	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1486014	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149411	0.88[ASW][hapmap];0.82[GIH][hapmap]
rs15756	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1632791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17125111	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2010630	0.82[ASN][1000 genomes]
rs2029145	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029146	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs224448	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs224575	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs2554863	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2630370	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2630371	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs319936	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap]
rs319939	0.94[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap]
rs370462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759405	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs427020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4438107	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs4768947	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55874804	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61934800	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580782	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580785	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6580788	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6580791	1.00[CHB][hapmap]
rs706805	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135399	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136960	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953867	1.00[CHB][hapmap]
rs7958068	0.82[EUR][1000 genomes]
rs7969803	0.84[EUR][1000 genomes]
rs7971308	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7976431	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977740	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829015	0.82[AMR][1000 genomes]
rs829025	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9739342	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs224572	DDN	cis	cerebellum	SCAN
rs224572	RND1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51399200-51418000	Weak transcription	Gastric	stomach
2	chr12:51401400-51417800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
5	chr12:51402400-51417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:51402400-51417600	Weak transcription	Left Ventricle	heart
7	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:51403400-51417600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:51403600-51417400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:51403600-51417600	Weak transcription	HSMM	muscle
12	chr12:51403800-51417000	Weak transcription	Brain Germinal Matrix	brain
13	chr12:51404800-51417800	Weak transcription	Fetal Brain Female	brain
14	chr12:51406400-51417200	Weak transcription	Fetal Brain Male	brain
15	chr12:51406400-51417400	Weak transcription	Osteobl	bone
16	chr12:51406400-51417600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:51407000-51417400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:51407000-51417600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:51407600-51417200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:51407600-51417600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:51408600-51417000	Weak transcription	Fetal Muscle Leg	muscle
23	chr12:51408600-51417000	Weak transcription	Psoas Muscle	Psoas
24	chr12:51409000-51417400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:51410800-51418400	Weak transcription	Primary B cells from cord blood	blood
26	chr12:51412200-51417800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:51412600-51418400	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:51412800-51416600	Enhancers	Brain Substantia Nigra	brain
29	chr12:51412800-51417800	Enhancers	Brain Cingulate Gyrus	brain
30	chr12:51412800-51418000	Enhancers	Primary T cells from cord blood	blood
31	chr12:51413000-51417200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:51413000-51417600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr12:51413200-51418400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr12:51413800-51416800	Flanking Active TSS	K562	blood
35	chr12:51413800-51418000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr12:51414000-51417600	Enhancers	HepG2	liver
37	chr12:51414200-51416600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:51414400-51417400	Enhancers	Liver	Liver
39	chr12:51414400-51418000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr12:51414600-51416600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:51414600-51417400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:51414800-51416800	Enhancers	Fetal Thymus	thymus
43	chr12:51414800-51417200	Weak transcription	Aorta	Aorta
44	chr12:51414800-51417400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:51415000-51417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:51415000-51417400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:51415000-51417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:51415200-51417200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr12:51415200-51417200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:51415200-51417600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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