Variant report

Variant	rs61700597
Chromosome Location	chr1:227423587-227423588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227421745..227423708-chr1:227616261..227618228,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242757	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10799411	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10916098	0.82[AMR][1000 genomes]
rs10916110	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916117	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12033050	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035190	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035998	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12038272	0.96[ASN][1000 genomes]
rs12073573	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12079122	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12079173	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12080452	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12095674	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12097121	0.82[AMR][1000 genomes]
rs4065211	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61834325	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61834563	0.88[EUR][1000 genomes]
rs61834564	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs645081	0.82[AMR][1000 genomes]
rs6660043	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6699534	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs688718	0.82[AMR][1000 genomes]
rs72757311	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513122	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
4	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
5	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
6	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227414000-227424400	Weak transcription	Psoas Muscle	Psoas
8	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227414200-227424200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:227414200-227424400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:227414200-227426800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:227414200-227453800	Weak transcription	HSMM	muscle
15	chr1:227414400-227423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:227415400-227424400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
22	chr1:227422000-227430800	Weak transcription	Ovary	ovary
23	chr1:227422200-227423600	Enhancers	Brain Anterior Caudate	brain
24	chr1:227422200-227423600	Enhancers	Brain Hippocampus Middle	brain
25	chr1:227422200-227423800	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:227422200-227424000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:227422400-227424000	Enhancers	K562	blood
28	chr1:227422600-227430800	Weak transcription	Gastric	stomach
29	chr1:227422800-227423600	Enhancers	Liver	Liver
30	chr1:227422800-227423600	Enhancers	Colon Smooth Muscle	Colon
31	chr1:227423000-227423600	Enhancers	Brain Substantia Nigra	brain
32	chr1:227423000-227424000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:227423000-227424400	Weak transcription	Left Ventricle	heart
34	chr1:227423000-227426800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:227423000-227432400	Weak transcription	Small Intestine	intestine
36	chr1:227423200-227423600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr1:227423200-227423600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr1:227423200-227424000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:227423200-227424400	Weak transcription	Stomach Mucosa	stomach
40	chr1:227423200-227427400	Weak transcription	A549	lung
41	chr1:227423400-227424400	Weak transcription	HUVEC	blood vessel
42	chr1:227423400-227426400	Weak transcription	Brain Angular Gyrus	brain

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