Variant report

Variant	rs12029680
Chromosome Location	chr1:47080741-47080742
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47079661..47082285-chr1:47135813..47137705,2	K562	blood:
2	chr1:47069390..47072755-chr1:47079314..47082367,4	MCF-7	breast:
3	chr1:47078421..47080865-chr1:47080975..47083544,2	MCF-7	breast:
4	chr1:47080354..47082092-chr1:47110886..47112430,2	MCF-7	breast:
5	chr1:47080724..47082396-chr1:47183672..47185631,2	MCF-7	breast:
6	chr1:47077660..47081751-chr1:47132686..47135354,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186118	Chromatin interaction
ENSG00000142961	Chromatin interaction
ENSG00000159658	Chromatin interaction
ENSG00000123472	Chromatin interaction
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1054743	0.89[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs10890405	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211306	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211309	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs11211312	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211317	0.86[ASN][1000 genomes]
rs11211328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047046	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12048342	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12093643	0.87[ASN][1000 genomes]
rs12138971	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1933934	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs3753359	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766231	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766236	0.82[CEU][hapmap];0.84[CHB][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs3766240	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs3818323	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55680528	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56869893	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59446321	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6429606	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7552833	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556307	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7556481	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs764803	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8602	0.90[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9659890	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9804164	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9804165	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv522319	chr1:47080741-47094267	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12029680	RIMKLA	cis	parietal	SCAN
rs12029680	C1orf84	cis	cerebellum	SCAN
rs12029680	CLDN19	cis	cerebellum	SCAN
rs12029680	MOB3C	cis	Whole Blood	GTEx
rs12029680	MPL	cis	parietal	SCAN
rs12029680	MKNK1	Cis_1M	lymphoblastoid	RTeQTL
rs12029680	MKNK1	cis	cerebellum	SCAN
rs12029680	C1orf223	cis	parietal	SCAN
rs12029680	MKNK1	cis	Whole Blood	GTEx
rs12029680	MKNK1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47070400-47081200	Weak transcription	Fetal Brain Male	brain
2	chr1:47076400-47081400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:47076800-47081800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr1:47077000-47081000	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr1:47077000-47081000	Enhancers	Brain Anterior Caudate	brain
6	chr1:47077000-47081200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:47077000-47081400	Enhancers	Left Ventricle	heart
8	chr1:47077000-47081400	Enhancers	Psoas Muscle	Psoas
9	chr1:47077000-47081600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:47077000-47082000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:47077200-47081200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:47077200-47081600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:47077400-47081200	Enhancers	HMEC	breast
14	chr1:47077600-47081600	Enhancers	Fetal Heart	heart
15	chr1:47078000-47081000	Enhancers	Hela-S3	cervix
16	chr1:47078000-47081400	Weak transcription	HUVEC	blood vessel
17	chr1:47078400-47081600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr1:47078600-47081000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:47078600-47081200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:47078800-47081200	Enhancers	Primary B cells from cord blood	blood
21	chr1:47078800-47081200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:47078800-47081200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:47078800-47081200	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:47078800-47081400	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:47078800-47081800	Enhancers	Spleen	Spleen
26	chr1:47079000-47080800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:47079000-47081000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:47079000-47081000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:47079000-47081000	Enhancers	NHDF-Ad	bronchial
30	chr1:47079000-47081200	Enhancers	Aorta	Aorta
31	chr1:47079000-47081200	Enhancers	Liver	Liver
32	chr1:47079000-47081200	Enhancers	Fetal Lung	lung
33	chr1:47079000-47081400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:47079000-47081400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:47079000-47081400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:47079000-47081400	Enhancers	Gastric	stomach
37	chr1:47079000-47081400	Enhancers	Stomach Mucosa	stomach
38	chr1:47079000-47081600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:47079000-47082000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:47079000-47082000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr1:47079200-47081000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:47079200-47081000	Enhancers	Primary T cells from cord blood	blood
43	chr1:47079200-47081000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:47079200-47081000	Enhancers	Placenta	Placenta
45	chr1:47079200-47081000	Enhancers	NHLF	lung
46	chr1:47079200-47081200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:47079200-47081200	Enhancers	Dnd41	blood
48	chr1:47079200-47081200	Enhancers	HSMMtube	muscle
49	chr1:47079200-47081400	Enhancers	Esophagus	oesophagus
50	chr1:47079200-47081400	Enhancers	Lung	lung

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