Variant report

Variant	rs6671527
Chromosome Location	chr1:47080679-47080680
allele	A/G
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	chr1:47076423..47078358-chr1:47078950..47080736,2	K562	blood:
6	chr1:47077660..47081751-chr1:47132686..47135354,3	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10890406	0.88[ASW][hapmap];0.93[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10890407	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10890408	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211319	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211320	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211323	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211324	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11211325	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11211326	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11211327	0.82[EUR][1000 genomes]
rs12022855	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136479	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1258012	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]
rs2297850	0.85[CEU][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap]
rs35494693	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36058295	0.88[EUR][1000 genomes]
rs4275405	0.91[CEU][hapmap]
rs4660357	0.93[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4660947	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6687832	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6704020	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7526249	0.87[EUR][1000 genomes]
rs7526328	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs942083	0.89[ASW][hapmap];0.93[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs956526	0.85[EUR][1000 genomes]
rs956527	0.93[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6671527	MMACHC	cis	cerebellum	SCAN
rs6671527	C1orf84	cis	cerebellum	SCAN

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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