Variant report

Variant	rs1541384
Chromosome Location	chr12:48045722-48045723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48044022..48046311-chr12:48051570..48054955,3	K562	blood:
2	chr12:48044527..48046603-chr12:48048041..48049724,2	K562	blood:
3	chr12:48045147..48046102-chr12:48080596..48081443,2	K562	blood:
4	chr12:48045249..48046046-chr12:48080121..48081065,3	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10783212	0.95[ASN][1000 genomes]
rs10875666	0.82[EUR][1000 genomes]
rs10875677	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875682	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875685	0.89[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap]
rs10875686	0.82[ASN][1000 genomes]
rs10875687	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs10875688	0.80[ASN][1000 genomes]
rs11168191	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168193	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168203	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168208	0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168214	0.80[ASN][1000 genomes]
rs11168215	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11168216	0.80[ASN][1000 genomes]
rs12366410	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12367193	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12370643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2072117	0.80[ASN][1000 genomes]
rs2240079	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2240080	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2283346	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764013	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.85[ASN][1000 genomes]
rs56011001	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56240307	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs582680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs583752	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs602143	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs604662	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs605499	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs611627	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs612773	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61917590	0.95[ASN][1000 genomes]
rs61917591	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61917594	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61917595	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61917616	0.80[ASN][1000 genomes]
rs61917617	0.80[ASN][1000 genomes]
rs622098	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs623894	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs630777	0.95[ASN][1000 genomes]
rs632944	0.95[ASN][1000 genomes]
rs634833	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs642453	0.85[EUR][1000 genomes]
rs644531	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs646223	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs652380	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs653136	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6580634	0.93[ASN][1000 genomes]
rs658567	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs659836	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs668968	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs671961	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs679789	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs687676	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7136143	0.82[EUR][1000 genomes]
rs7136561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137529	0.97[ASN][1000 genomes]
rs7311663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7316761	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs739858	0.82[EUR][1000 genomes]
rs7484827	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7954502	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7968783	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7969186	0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7976748	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs7977613	0.97[ASN][1000 genomes]
rs7977786	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs864112	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv521329	chr12:48044011-48051456	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1541384	DNAJC22	cis	parietal	SCAN
rs1541384	YAF2	cis	cerebellum	SCAN
rs1541384	RPAP3	cis	cerebellum	SCAN
rs1541384	ENDOU	cis	Thyroid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48007400-48055400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:48015600-48055200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:48029400-48055400	Weak transcription	Thymus	Thymus
4	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:48031000-48083200	Weak transcription	Esophagus	oesophagus
6	chr12:48031200-48051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:48031200-48053200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48031400-48046200	Weak transcription	Fetal Stomach	stomach
9	chr12:48031400-48058400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48032200-48045800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:48036600-48055400	Weak transcription	Ovary	ovary
12	chr12:48038200-48059400	Weak transcription	Small Intestine	intestine
13	chr12:48038600-48051400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:48038800-48045800	Weak transcription	Primary T cells from cord blood	blood
15	chr12:48038800-48046000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:48039000-48052800	Weak transcription	Dnd41	blood
17	chr12:48039200-48046000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:48039200-48046200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:48039200-48052800	Weak transcription	Fetal Intestine Large	intestine
20	chr12:48039400-48058400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:48040000-48051400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:48040200-48050000	Weak transcription	Primary B cells from cord blood	blood
23	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
24	chr12:48042200-48058400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:48042400-48046000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:48042400-48046000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:48042400-48060200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:48042600-48046200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:48042600-48054800	Weak transcription	Placenta	Placenta
30	chr12:48042800-48046200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:48043000-48045800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:48043200-48046400	Weak transcription	K562	blood
33	chr12:48043200-48054600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:48043400-48080000	Weak transcription	NHEK	skin
35	chr12:48043800-48053600	Weak transcription	Left Ventricle	heart
36	chr12:48043800-48055600	Weak transcription	Right Ventricle	heart
37	chr12:48044000-48046800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:48044200-48046000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:48044200-48046600	Enhancers	GM12878-XiMat	blood
40	chr12:48044200-48046800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:48044400-48046600	Enhancers	Rectal Smooth Muscle	rectum
42	chr12:48044400-48046800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr12:48044600-48046000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:48044600-48046600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:48044600-48046600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr12:48044600-48046800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr12:48044600-48046800	Enhancers	HSMM	muscle
48	chr12:48044800-48046800	Enhancers	Brain Cingulate Gyrus	brain
49	chr12:48044800-48046800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr12:48044800-48047000	Enhancers	Colon Smooth Muscle	Colon

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