Variant report

Variant	rs7975560
Chromosome Location	chr12:62875839-62875840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62870116..62872477-chr12:62874271..62877782,4	K562	blood:
2	chr12:62874210..62877124-chr12:62898589..62900755,2	K562	blood:
3	chr12:62873316..62875868-chr12:62879618..62881508,2	MCF-7	breast:
4	chr12:62874817..62876919-chr12:62877529..62879256,2	MCF-7	breast:
5	chr12:62870116..62872263-chr12:62874889..62877782,3	K562	blood:
6	chr12:62874375..62877200-chr12:62880346..62883234,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257568	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10128830	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10128959	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10161549	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10219555	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10219765	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10735907	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10735909	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747963	0.89[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs10747965	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10747966	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784302	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784303	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784306	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10784307	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10877851	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10877860	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877863	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877865	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877868	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877869	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877872	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10877873	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877876	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10877878	0.86[EUR][1000 genomes]
rs10877880	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877883	0.84[CEU][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10877885	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877886	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877887	0.81[ASN][1000 genomes]
rs10877888	0.90[CHB][hapmap];0.84[MEX][hapmap]
rs11174493	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174497	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174507	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174513	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11174534	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174538	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11174539	0.87[EUR][1000 genomes]
rs11174540	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174541	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174542	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174550	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11495588	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12227568	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12300696	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12305077	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12308140	0.82[MKK][hapmap]
rs12309683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12357	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12371971	0.90[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs12371972	0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[ASN][1000 genomes]
rs12578200	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580048	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12581171	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12809279	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810119	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12829103	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1498713	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029937	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2047478	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2047479	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2141777	0.95[ASN][1000 genomes]
rs2220980	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35409044	0.82[EUR][1000 genomes]
rs4763021	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763174	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4763177	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4763179	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4763180	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581452	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581454	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7134302	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136993	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71453871	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7294404	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308021	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7316612	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7957417	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7963657	0.85[CEU][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7975183	0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7975560	PPM1H	cis	parietal	SCAN
rs7975560	MON2	cis	multi-tissue	Pritchard
rs7975560	TBK1	cis	cerebellum	SCAN
rs7975560	MON2	cis	parietal	SCAN
rs7975560	NXPH4	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62861800-62879800	Weak transcription	HSMMtube	muscle
2	chr12:62861800-62902200	Weak transcription	Fetal Kidney	kidney
3	chr12:62862800-62895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:62863200-62876000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:62863200-62879400	Weak transcription	Thymus	Thymus
6	chr12:62863200-62881400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:62863200-62895200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:62863200-62896800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:62863200-62901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
11	chr12:62863400-62877600	Weak transcription	A549	lung
12	chr12:62863400-62878200	Weak transcription	Fetal Lung	lung
13	chr12:62863400-62895400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:62863400-62902000	Weak transcription	HUVEC	blood vessel
15	chr12:62863400-62911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:62863600-62877400	Weak transcription	NHEK	skin
17	chr12:62863600-62892600	Weak transcription	NH-A	brain
18	chr12:62863600-62926400	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:62864000-62878800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:62864000-62894400	Weak transcription	Spleen	Spleen
21	chr12:62864000-62899200	Weak transcription	Brain Germinal Matrix	brain
22	chr12:62864000-62901600	Weak transcription	Lung	lung
23	chr12:62864000-62901600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:62864000-62906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:62865800-62876000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:62866000-62892000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:62866000-62895400	Weak transcription	Left Ventricle	heart
28	chr12:62866200-62887400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:62866200-62897000	Weak transcription	K562	blood
30	chr12:62866200-62899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:62866200-62906200	Weak transcription	Aorta	Aorta
32	chr12:62866600-62877600	Weak transcription	NHDF-Ad	bronchial
33	chr12:62866600-62896000	Weak transcription	Fetal Brain Female	brain
34	chr12:62866600-62906200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:62866600-62912400	Weak transcription	NHLF	lung
36	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
37	chr12:62866800-62883800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:62866800-62888400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:62867000-62890200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:62867200-62898600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:62869000-62892000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:62869000-62904400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:62869600-62876200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:62870400-62876400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:62871000-62910800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:62871200-62895200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:62871800-62876600	Weak transcription	Ovary	ovary
48	chr12:62871800-62877600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:62871800-62878600	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:62871800-62878800	Weak transcription	Fetal Stomach	stomach

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