Variant report

Variant	rs35952573
Chromosome Location	chr1:227398288-227398289
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	chr1:227396969..227399919-chr1:227412592..227414970,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10916112	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916113	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916116	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916125	0.96[AMR][1000 genomes]
rs11576239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11584325	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11585910	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12119153	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12123597	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12128174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131061	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12131459	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131933	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12133230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138092	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12138364	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138664	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12144205	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12746316	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12754677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755770	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513607	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1513613	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17613235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063661	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28648445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34113967	1.00[AMR][1000 genomes]
rs34702208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35160496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4308948	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61834323	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61834324	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61834326	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61834590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834625	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61834626	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6660168	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675572	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6678714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697583	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7512871	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7518813	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7523759	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7539662	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7543419	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7548118	1.00[AMR][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	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
2	chr1:227343200-227400400	Weak transcription	A549	lung
3	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
6	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
11	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
12	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:227374400-227401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:227374600-227401600	Weak transcription	Left Ventricle	heart
15	chr1:227375600-227410800	Weak transcription	HepG2	liver
16	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
17	chr1:227378400-227401000	Weak transcription	Placenta	Placenta
18	chr1:227379600-227399200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:227380200-227402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:227380200-227405200	Weak transcription	Gastric	stomach
21	chr1:227380200-227421800	Weak transcription	Ovary	ovary
22	chr1:227380400-227400000	Weak transcription	HSMMtube	muscle
23	chr1:227380400-227400000	Weak transcription	NHEK	skin
24	chr1:227380400-227404000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:227380400-227406800	Weak transcription	NHDF-Ad	bronchial
26	chr1:227380800-227398400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:227381600-227406600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:227382000-227414000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:227382600-227398400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:227385000-227400000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
33	chr1:227386400-227413800	Weak transcription	Brain Anterior Caudate	brain
34	chr1:227386800-227399400	Weak transcription	HUVEC	blood vessel
35	chr1:227386800-227406600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:227387000-227413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:227387400-227414000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:227390600-227413600	Weak transcription	Small Intestine	intestine
39	chr1:227396800-227413600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:227397000-227406800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:227397400-227399800	Weak transcription	Fetal Brain Male	brain
42	chr1:227397400-227399800	Weak transcription	NH-A	brain
43	chr1:227397800-227398800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:227397800-227399400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:227397800-227399800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:227397800-227400400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:227397800-227400400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:227398000-227398400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:227398000-227398800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
50	chr1:227398000-227398800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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