Variant report

Variant	rs1196804
Chromosome Location	chr12:105539384-105539385
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105534493..105537599-chr12:105538790..105541931,3	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10861327	0.85[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs10861328	0.85[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs10861329	0.85[CEU][hapmap]
rs10861330	0.85[CEU][hapmap]
rs10861335	0.85[CEU][hapmap]
rs10861336	0.85[CEU][hapmap]
rs1109432	0.91[EUR][1000 genomes]
rs11112347	0.85[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap]
rs11112350	0.85[CEU][hapmap]
rs11112351	0.85[CEU][hapmap]
rs11112414	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11610656	0.84[ASN][1000 genomes]
rs11612252	0.85[CEU][hapmap]
rs11613261	0.85[CEU][hapmap]
rs1196750	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1196752	0.85[AFR][1000 genomes]
rs1196758	0.96[CEU][hapmap]
rs1196766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196767	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196768	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs1196776	0.91[EUR][1000 genomes]
rs1196778	0.91[EUR][1000 genomes]
rs1196779	0.89[EUR][1000 genomes]
rs1196781	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1196785	0.84[EUR][1000 genomes]
rs1196788	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs1196796	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1196803	0.99[ASN][1000 genomes]
rs1196809	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196810	0.98[ASN][1000 genomes]
rs1196812	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1196814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196816	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs1196821	0.94[ASN][1000 genomes]
rs1196822	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196826	0.96[ASN][1000 genomes]
rs1196827	0.96[ASN][1000 genomes]
rs1196828	0.96[ASN][1000 genomes]
rs1196829	0.96[ASN][1000 genomes]
rs1196835	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1196836	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196837	0.95[ASN][1000 genomes]
rs1196838	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196840	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1196843	0.92[ASN][1000 genomes]
rs1196846	0.96[ASN][1000 genomes]
rs1196850	0.94[ASN][1000 genomes]
rs1196854	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196855	0.94[ASN][1000 genomes]
rs1196856	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196858	0.95[ASN][1000 genomes]
rs1196860	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196865	0.91[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196866	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196867	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196868	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196870	0.99[ASN][1000 genomes]
rs1196876	0.99[ASN][1000 genomes]
rs1196877	0.99[ASN][1000 genomes]
rs1196878	0.96[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196880	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1196882	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs1196883	0.86[CHD][hapmap]
rs1201657	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1201658	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12581638	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs17036869	0.81[CHB][hapmap]
rs1732371	0.93[ASN][1000 genomes]
rs1732377	0.80[EUR][1000 genomes]
rs1732378	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1732379	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1732384	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2246510	0.96[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2264066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2374448	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2440693	0.80[EUR][1000 genomes]
rs2440708	1.00[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs2440713	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2440717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440719	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4144468	0.85[CEU][hapmap]
rs4964127	0.84[EUR][1000 genomes]
rs4964346	0.82[EUR][1000 genomes]
rs6539196	0.83[EUR][1000 genomes]
rs727888	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs7308195	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs7309320	0.83[EUR][1000 genomes]
rs7310488	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs7969800	0.83[EUR][1000 genomes]
rs9143	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	esv1826054	chr12:105505809-105568176	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1049296	chr12:105518764-105566079	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1196804	APPL2	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105503800-105544200	Weak transcription	Aorta	Aorta
2	chr12:105505200-105542600	Strong transcription	Fetal Thymus	thymus
3	chr12:105505200-105559800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:105505200-105564000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:105505200-105567400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:105505200-105573000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:105505600-105550000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr12:105505600-105573200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:105505800-105571400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr12:105506400-105544600	Strong transcription	NHDF-Ad	bronchial
11	chr12:105506400-105573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:105506600-105549200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:105506800-105568800	Strong transcription	Dnd41	blood
14	chr12:105506800-105572400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:105507000-105573200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr12:105507200-105571400	Strong transcription	Primary B cells from peripheral blood	blood
17	chr12:105507400-105565600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:105507600-105571400	Strong transcription	HUVEC	blood vessel
19	chr12:105507600-105572800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:105507800-105563800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:105507800-105573200	Strong transcription	Placenta	Placenta
22	chr12:105508000-105549200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:105508000-105550400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:105508000-105565400	Strong transcription	Adipose Nuclei	Adipose
25	chr12:105508200-105572800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:105508400-105562000	Strong transcription	Primary B cells from cord blood	blood
27	chr12:105508600-105573000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:105508800-105565000	Strong transcription	Liver	Liver
29	chr12:105510000-105565200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:105513800-105567800	Weak transcription	Pancreas	Pancrea
31	chr12:105515200-105557600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:105517600-105540600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:105517800-105555200	Weak transcription	Small Intestine	intestine
34	chr12:105518600-105573200	Strong transcription	HSMM	muscle
35	chr12:105519400-105558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:105520000-105550000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:105522600-105557600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:105522600-105586000	Weak transcription	Stomach Mucosa	stomach
39	chr12:105522800-105548200	Weak transcription	Brain Angular Gyrus	brain
40	chr12:105524600-105578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:105525400-105546800	Weak transcription	Colonic Mucosa	Colon
42	chr12:105525400-105583200	Weak transcription	Fetal Heart	heart
43	chr12:105525600-105549000	Weak transcription	Right Ventricle	heart
44	chr12:105526200-105544200	Weak transcription	Lung	lung
45	chr12:105527000-105544200	Weak transcription	Fetal Intestine Small	intestine
46	chr12:105527000-105544200	Weak transcription	Fetal Stomach	stomach
47	chr12:105527000-105544200	Weak transcription	Spleen	Spleen
48	chr12:105527200-105565400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:105528800-105549800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:105529600-105543800	Weak transcription	Fetal Brain Male	brain

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