Variant report

Variant	rs1258012
Chromosome Location	chr1:47072144-47072145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:47072079-47072287	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:47071960-47072381	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47069390..47072755-chr1:47079314..47082367,4	MCF-7	breast:
2	chr1:47041661..47043778-chr1:47070091..47072496,2	K562	blood:
3	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:
4	chr1:47069986..47078443-chr1:47078833..47084050,15	K562	blood:
5	chr1:47066512..47069474-chr1:47070954..47073416,4	K562	blood:
6	chr1:47069954..47072526-chr1:47696601..47699407,3	K562	blood:

No data

Variant related genes	Relation type
MKNK1	TF binding region
ENSG00000142961	Chromatin interaction
ENSG00000162367	Chromatin interaction
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10890406	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890407	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10890408	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211319	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211320	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211323	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211325	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211326	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11211327	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12022855	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136479	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1258010	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258022	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258050	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258051	1.00[CHB][hapmap]
rs1767612	1.00[CHB][hapmap]
rs2297850	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs35494693	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36058295	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275405	1.00[CEU][hapmap]
rs4660357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660947	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671527	0.89[ASW][hapmap];0.93[CEU][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6687832	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704020	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526249	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7526328	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs942083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs946321	1.00[CHB][hapmap]
rs956526	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs956527	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1258012	FAM183A	cis	cerebellum	SCAN
rs1258012	C1orf84	cis	cerebellum	SCAN
rs1258012	MMACHC	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47070000-47077600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:47070000-47078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47070200-47073200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:47070400-47073600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:47070400-47073600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:47070400-47073800	Weak transcription	Brain Germinal Matrix	brain
7	chr1:47070400-47081200	Weak transcription	Fetal Brain Male	brain
8	chr1:47070600-47072200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:47070600-47072200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:47070600-47072600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:47070600-47073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:47070600-47073200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:47070600-47073200	Weak transcription	Aorta	Aorta
14	chr1:47070600-47073200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:47070600-47073200	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:47070600-47073400	Weak transcription	Fetal Intestine Large	intestine
17	chr1:47070600-47073600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:47070600-47073600	Weak transcription	Esophagus	oesophagus
19	chr1:47070600-47073600	Weak transcription	Gastric	stomach
20	chr1:47070600-47073800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:47070600-47073800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:47070600-47073800	Weak transcription	Fetal Lung	lung
23	chr1:47070600-47073800	Enhancers	Psoas Muscle	Psoas
24	chr1:47070600-47074000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:47070600-47074000	Weak transcription	Fetal Kidney	kidney
26	chr1:47070600-47074600	Weak transcription	HSMM	muscle
27	chr1:47070600-47077200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:47070600-47077400	Weak transcription	NH-A	brain
29	chr1:47070600-47077600	Weak transcription	Fetal Heart	heart
30	chr1:47070600-47078400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:47070800-47072200	Enhancers	Primary T cells from cord blood	blood
32	chr1:47070800-47072200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:47070800-47072400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:47070800-47073000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:47070800-47073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:47070800-47073400	Weak transcription	Colonic Mucosa	Colon
37	chr1:47070800-47073400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:47070800-47073400	Enhancers	NHEK	skin
39	chr1:47070800-47073600	Weak transcription	Brain Anterior Caudate	brain
40	chr1:47070800-47073600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:47070800-47073800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:47070800-47073800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:47070800-47073800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:47070800-47073800	Weak transcription	HSMMtube	muscle
45	chr1:47070800-47074000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:47070800-47074000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:47070800-47074000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:47070800-47074000	Weak transcription	NHLF	lung
49	chr1:47070800-47074200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:47070800-47074400	Weak transcription	H1 Cell Line	embryonic stem cell

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