Variant report

Variant	rs10219555
Chromosome Location	chr12:62928633-62928634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62927109..62929930-chr12:63090186..63092753,2	K562	blood:
2	chr12:62919040..62922013-chr12:62927125..62929427,2	K562	blood:
3	chr12:62920513..62925358-chr12:62927927..62931461,4	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10128830	0.94[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10128959	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10161549	0.94[ASW][hapmap];0.84[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10219765	0.80[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10735907	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10735909	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10747963	0.82[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs10747965	0.86[ASN][1000 genomes]
rs10747966	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10784299	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784302	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10784303	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10784306	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10784307	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877851	0.87[ASN][1000 genomes]
rs10877860	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877863	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877865	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877866	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877868	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877869	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877872	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10877873	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877876	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877878	0.91[EUR][1000 genomes]
rs10877880	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877882	0.80[EUR][1000 genomes]
rs10877883	0.84[CEU][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10877885	0.94[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877886	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877887	0.86[ASN][1000 genomes]
rs10877888	0.85[CHB][hapmap];0.87[MKK][hapmap]
rs11174493	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11174497	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11174507	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174513	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11174520	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174534	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11174538	0.81[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11174539	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11174540	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11174541	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11174542	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11174545	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11174550	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11495588	0.91[ASN][1000 genomes]
rs12227568	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12300696	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12305077	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12308140	0.93[MKK][hapmap]
rs12309683	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12357	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12371971	0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs12371972	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs12578200	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12580048	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581171	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12809279	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12810119	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12829103	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498713	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2029937	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2047478	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2047479	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141777	0.89[ASN][1000 genomes]
rs2220980	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35409044	0.86[EUR][1000 genomes]
rs4763021	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4763174	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763177	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763179	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4763180	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581452	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581454	0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7134302	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136993	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71453871	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294404	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7298782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302027	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308021	0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.89[ASN][1000 genomes]
rs7316612	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957417	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958597	0.81[ASN][1000 genomes]
rs7963657	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7975183	1.00[ASW][hapmap];0.90[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975560	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]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv469418	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv559156	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10219555	PPM1H	cis	parietal	SCAN
rs10219555	TBK1	cis	cerebellum	SCAN
rs10219555	NXPH4	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
2	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
3	chr12:62876000-62937400	Weak transcription	Gastric	stomach
4	chr12:62889200-62949600	Weak transcription	Small Intestine	intestine
5	chr12:62897600-62931000	Weak transcription	K562	blood
6	chr12:62897600-62944000	Weak transcription	Esophagus	oesophagus
7	chr12:62902400-62929200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:62903600-62949800	Weak transcription	NHEK	skin
9	chr12:62904600-62929200	Weak transcription	HUVEC	blood vessel
10	chr12:62906400-62943800	Weak transcription	Aorta	Aorta
11	chr12:62906600-62931600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:62907000-62931000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:62907000-62987200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:62907400-62940200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:62908400-62931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:62911400-62944000	Weak transcription	Spleen	Spleen
17	chr12:62911800-62930400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:62914200-62941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:62915800-62930200	Weak transcription	Fetal Stomach	stomach
20	chr12:62915800-62971600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:62917000-62940600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
23	chr12:62917400-62960000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:62917800-62930200	Weak transcription	Fetal Intestine Small	intestine
25	chr12:62919400-62937200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:62919600-62937200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:62919800-62970000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr12:62920000-62950200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:62924400-62931000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:62924400-62945600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:62924400-62949800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:62924400-62969800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:62924600-62938600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:62924800-62931400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:62924800-62967600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:62925400-62949800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:62925800-62930200	Strong transcription	Osteobl	bone
38	chr12:62925800-62931200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:62925800-62932400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:62925800-62933600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:62926000-62934400	Strong transcription	Dnd41	blood
42	chr12:62926000-62945000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:62926000-62951400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:62926200-62929600	Strong transcription	Brain Anterior Caudate	brain
45	chr12:62926200-62929800	Strong transcription	GM12878-XiMat	blood
46	chr12:62926200-62930400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:62926200-62931000	Strong transcription	Adipose Nuclei	Adipose
48	chr12:62926200-62931000	Strong transcription	NHDF-Ad	bronchial
49	chr12:62926200-62931200	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:62926200-62932400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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