Variant report

Variant	rs6673144
Chromosome Location	chr1:179890655-179890656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179889909..179891977-chr1:179899561..179901875,2	K562	blood:
2	chr1:179885300..179888007-chr1:179889040..179891794,2	MCF-7	breast:
3	chr1:179890511..179892011-chr1:179902778..179905230,2	MCF-7	breast:
4	chr1:179885633..179888323-chr1:179889442..179891149,2	K562	blood:
5	chr1:179889749..179892017-chr1:179923918..179925424,2	MCF-7	breast:
6	chr1:179850249..179852659-chr1:179890266..179891877,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1048418	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10494523	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10913894	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10913895	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10913905	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10913909	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119431	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12121694	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12126625	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12136091	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12136465	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12143942	0.89[CEU][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12144991	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16854910	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3845388	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4301600	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61740391	0.92[EUR][1000 genomes]
rs6425596	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659939	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72708661	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72708662	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7527215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7531195	0.91[CEU][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7545581	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7549317	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9726605	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	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
2	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
3	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
4	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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
3	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
4	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr1:179868400-179890800	Strong transcription	Dnd41	blood
6	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:179869200-179891600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:179869400-179891400	Strong transcription	Liver	Liver
10	chr1:179871200-179891000	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:179873400-179891400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:179875200-179891800	Strong transcription	Primary B cells from cord blood	blood
13	chr1:179876000-179891200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:179877000-179891600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:179879600-179890800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:179880800-179891000	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:179881000-179891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:179881800-179891200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:179882000-179891600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:179882600-179890800	Strong transcription	Colon Smooth Muscle	Colon
21	chr1:179886400-179891600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:179886800-179891200	Strong transcription	GM12878-XiMat	blood
23	chr1:179887200-179893400	Weak transcription	Pancreas	Pancrea
24	chr1:179887200-179897200	Weak transcription	Fetal Intestine Small	intestine
25	chr1:179887400-179890800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:179887400-179891400	Weak transcription	Psoas Muscle	Psoas
27	chr1:179887400-179891600	Weak transcription	Spleen	Spleen
28	chr1:179887400-179892800	Weak transcription	Gastric	stomach
29	chr1:179887400-179894600	Weak transcription	HSMMtube	muscle
30	chr1:179887400-179897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:179887400-179897600	Weak transcription	Aorta	Aorta
32	chr1:179887400-179898600	Weak transcription	Right Ventricle	heart
33	chr1:179887400-179899200	Weak transcription	Small Intestine	intestine
34	chr1:179887400-179900600	Weak transcription	Ovary	ovary
35	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:179887600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:179887600-179899400	Weak transcription	K562	blood
38	chr1:179887800-179892000	Weak transcription	Fetal Heart	heart
39	chr1:179887800-179892200	Weak transcription	Colonic Mucosa	Colon
40	chr1:179887800-179893000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:179887800-179899400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:179888000-179891600	Weak transcription	NH-A	brain
43	chr1:179888000-179894600	Weak transcription	HMEC	breast
44	chr1:179888200-179892200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:179888200-179892400	Weak transcription	Fetal Brain Female	brain
46	chr1:179888600-179890800	Weak transcription	Brain Angular Gyrus	brain
47	chr1:179888600-179890800	Weak transcription	Brain Anterior Caudate	brain
48	chr1:179888600-179892000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:179888600-179892000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:179888600-179892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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