Variant report

Variant	rs1281412
Chromosome Location	chr1:179818132-179818133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179815555..179818166-chr1:179820853..179822407,2	MCF-7	breast:
2	chr1:179810244..179812885-chr1:179816877..179820145,3	K562	blood:
3	chr1:179811427..179813189-chr1:179817420..179819115,2	MCF-7	breast:
4	chr1:179813084..179815774-chr1:179817497..179820242,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10913901	0.81[EUR][1000 genomes]
rs1144575	0.81[ASN][1000 genomes]
rs1148812	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1148815	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12062341	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12062383	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281378	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281408	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1281411	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1281413	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281428	0.83[ASN][1000 genomes]
rs1281429	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281430	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281432	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1298479	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1300068	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2007148	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2245425	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2249346	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2762858	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2777908	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2777909	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2777917	0.89[AMR][1000 genomes]
rs2794582	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2794583	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs474258	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs475233	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs475434	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs479094	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs480377	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs480498	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs501300	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs505789	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs505837	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs514421	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs518774	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs522534	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs530369	0.86[AMR][1000 genomes]
rs530854	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs538512	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs547776	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs549650	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs553830	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs555270	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs589780	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs599185	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs600046	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs600553	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs605807	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609521	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs612215	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs644412	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:179802600-179819800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:179803600-179833600	Weak transcription	Fetal Brain Male	brain
5	chr1:179805800-179818200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:179807600-179827400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:179807800-179833800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:179808600-179822600	Strong transcription	Fetal Intestine Large	intestine
9	chr1:179808600-179837000	Strong transcription	Liver	Liver
10	chr1:179808600-179839800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:179808800-179836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:179809200-179821600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:179809800-179827800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:179810200-179828000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:179812000-179822000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:179812200-179827800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:179812400-179820400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr1:179812600-179821800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:179812600-179842600	Weak transcription	Stomach Mucosa	stomach
20	chr1:179812800-179821000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:179812800-179821400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:179812800-179822000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:179812800-179822600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:179813000-179822000	Strong transcription	Adipose Nuclei	Adipose
25	chr1:179813000-179822600	Strong transcription	Placenta	Placenta
26	chr1:179813200-179821000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:179813200-179821000	Strong transcription	GM12878-XiMat	blood
28	chr1:179813200-179822000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:179813200-179822000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:179813200-179822200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:179813200-179822200	Strong transcription	Dnd41	blood
32	chr1:179813200-179822600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:179813200-179823000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:179813200-179823400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:179813200-179839200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:179813400-179821000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:179813400-179821800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:179813400-179825400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:179813400-179834000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:179813600-179821000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr1:179814000-179822000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:179814000-179822000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:179814000-179822000	Strong transcription	HUVEC	blood vessel
44	chr1:179814200-179821000	Strong transcription	NH-A	brain
45	chr1:179814200-179821200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:179814200-179823600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:179814200-179834400	Weak transcription	Fetal Heart	heart
48	chr1:179814400-179820400	Strong transcription	HMEC	breast
49	chr1:179814400-179822200	Strong transcription	Osteobl	bone
50	chr1:179814400-179839200	Strong transcription	HSMM	muscle

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