Variant report

Variant	rs6667487
Chromosome Location	chr1:228874078-228874079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228827485..228830418-chr1:228872715..228875379,2	MCF-7	breast:
2	chr1:228870974..228874192-chr1:229289899..229293413,3	MCF-7	breast:
3	chr1:228872086..228874934-chr1:228877939..228879672,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12047916	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12065058	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12402303	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16848862	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4531263	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6660442	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7518941	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527878	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3336770	chr1:228873688-228874112	Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228870200-228875400	Active TSS	Brain Angular Gyrus	brain
2	chr1:228870400-228874200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr1:228870600-228874200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:228870600-228874400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:228870600-228875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:228872400-228875400	Weak transcription	Lung	lung
7	chr1:228872400-228875400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:228872400-228876400	Weak transcription	Hela-S3	cervix
9	chr1:228872400-228880200	Weak transcription	Left Ventricle	heart
10	chr1:228872600-228875400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:228872600-228877800	Weak transcription	Primary T cells from cord blood	blood
12	chr1:228872600-228878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:228872600-228880600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:228872600-228881200	Weak transcription	Esophagus	oesophagus
15	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:228872800-228874200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr1:228873000-228874600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:228873000-228875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:228873200-228874200	Enhancers	Fetal Brain Male	brain
20	chr1:228873200-228878400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:228873200-228879000	Weak transcription	Ovary	ovary
22	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:228873400-228874200	Transcr. at gene 5' and 3'	Placenta	Placenta
24	chr1:228873400-228874400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
25	chr1:228873400-228874600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:228873400-228876400	Weak transcription	Fetal Kidney	kidney
27	chr1:228873400-228876400	Enhancers	Stomach Mucosa	stomach
28	chr1:228873400-228879000	Weak transcription	Small Intestine	intestine
29	chr1:228873600-228874200	Genic enhancers	Colon Smooth Muscle	Colon
30	chr1:228873600-228874200	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
31	chr1:228873600-228875000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:228873600-228875400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:228873600-228875400	Weak transcription	Gastric	stomach
34	chr1:228873600-228875600	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
35	chr1:228873600-228876000	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
36	chr1:228873600-228876200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:228873600-228876600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:228873600-228876600	Genic enhancers	Pancreas	Pancrea
39	chr1:228873600-228877000	Genic enhancers	HepG2	liver
40	chr1:228873600-228877200	Genic enhancers	Fetal Thymus	thymus
41	chr1:228873600-228878000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:228873600-228878000	Weak transcription	Brain Germinal Matrix	brain
43	chr1:228873600-228878400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:228873600-228878400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:228873600-228879000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:228873600-228879000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:228873800-228874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:228873800-228874200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
49	chr1:228873800-228874200	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr1:228873800-228874200	Enhancers	Right Ventricle	heart

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