Variant report

Variant	rs6704020
Chromosome Location	chr1:47077871-47077872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47038329..47041159-chr1:47076859..47079950,3	K562	blood:
2	chr1:47076423..47078358-chr1:47078950..47080736,2	K562	blood:
3	chr1:47069986..47078443-chr1:47078833..47084050,15	K562	blood:
4	chr1:47076372..47077998-chr1:47081532..47083963,2	MCF-7	breast:
5	chr1:47068458..47072661-chr1:47073535..47079342,7	MCF-7	breast:
6	chr1:47048260..47050517-chr1:47077583..47079223,2	K562	blood:
7	chr1:47077660..47081751-chr1:47132686..47135354,3	MCF-7	breast:

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

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10890406	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890407	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10890408	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211319	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211320	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211323	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211324	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211325	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211326	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211327	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12022855	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12136479	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1258012	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297850	0.87[AMR][1000 genomes]
rs35494693	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36058295	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660357	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660947	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671527	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6687832	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526249	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7526328	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs942083	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956526	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs956527	0.93[AMR][1000 genomes];0.95[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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47070000-47078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:47070400-47081200	Weak transcription	Fetal Brain Male	brain
3	chr1:47070600-47078400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:47071000-47078400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:47071800-47079200	Weak transcription	Dnd41	blood
6	chr1:47072000-47079000	Strong transcription	Fetal Intestine Small	intestine
7	chr1:47073400-47079000	Strong transcription	Fetal Intestine Large	intestine
8	chr1:47073600-47078200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:47074000-47078800	Strong transcription	NHLF	lung
10	chr1:47074200-47079000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:47075000-47079800	Weak transcription	Fetal Kidney	kidney
12	chr1:47075200-47078800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:47075800-47078400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:47075800-47078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:47075800-47078800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:47075800-47079000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:47075800-47079000	Weak transcription	Brain Angular Gyrus	brain
18	chr1:47075800-47079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:47076000-47079000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:47076000-47079000	Weak transcription	Fetal Lung	lung
21	chr1:47076200-47078800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:47076400-47081400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:47076600-47078200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:47076600-47078800	Genic enhancers	Rectal Mucosa Donor 29	rectum
25	chr1:47076600-47079000	Genic enhancers	Placenta	Placenta
26	chr1:47076800-47078000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr1:47076800-47078000	Enhancers	Colon Smooth Muscle	Colon
28	chr1:47076800-47078600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:47076800-47078800	Genic enhancers	Spleen	Spleen
30	chr1:47076800-47079000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr1:47076800-47079000	Enhancers	Brain Hippocampus Middle	brain
32	chr1:47076800-47080400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr1:47076800-47081800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr1:47077000-47078000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:47077000-47078000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:47077000-47078000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:47077000-47078000	Genic enhancers	Liver	Liver
38	chr1:47077000-47078000	Enhancers	Stomach Mucosa	stomach
39	chr1:47077000-47078000	Flanking Active TSS	Hela-S3	cervix
40	chr1:47077000-47078200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr1:47077000-47078200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:47077000-47078200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr1:47077000-47078200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr1:47077000-47078600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:47077000-47078600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:47077000-47078800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr1:47077000-47078800	Weak transcription	Primary B cells from cord blood	blood
48	chr1:47077000-47078800	Genic enhancers	Duodenum Mucosa	Duodenum
49	chr1:47077000-47078800	Genic enhancers	Fetal Muscle Trunk	muscle
50	chr1:47077000-47079000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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