Variant report

Variant	rs7543579
Chromosome Location	chr1:227377699-227377700
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227373675..227376391-chr1:227377073..227380557,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10495253	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10799381	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916080	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916104	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12039370	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12139758	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1320494	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1483	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929858	0.85[AMR][1000 genomes]
rs2102634	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2482454	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2492630	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2670462	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2670471	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2718193	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2813947	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2813948	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2813950	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2813965	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2813967	0.83[EUR][1000 genomes]
rs2813969	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2813970	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3754418	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4351610	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4500279	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4653479	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4653813	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs485234	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs488104	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs498020	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56219094	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61834571	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs648877	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6662583	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6682472	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6682642	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6685823	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6692080	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6697665	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6699828	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689094	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs694740	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7412928	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7512409	0.83[AMR][1000 genomes]
rs7521110	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7523167	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549520	0.87[AMR][1000 genomes];0.83[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	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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
4	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:227343200-227400400	Weak transcription	A549	lung
7	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
11	chr1:227347200-227378000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:227348200-227377800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:227348200-227377800	Weak transcription	HUVEC	blood vessel
16	chr1:227348200-227379800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:227348400-227378000	Weak transcription	Liver	Liver
23	chr1:227355400-227379800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:227359200-227379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:227359400-227379800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:227359400-227379800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:227359400-227379800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
30	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
31	chr1:227362800-227377800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:227362800-227379800	Weak transcription	NHLF	lung
33	chr1:227363000-227379600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:227363800-227380600	Weak transcription	Esophagus	oesophagus
35	chr1:227364000-227379800	Weak transcription	HSMMtube	muscle
36	chr1:227364000-227385800	Weak transcription	Fetal Stomach	stomach
37	chr1:227364200-227381000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
39	chr1:227369000-227379600	Weak transcription	HMEC	breast
40	chr1:227369200-227382600	Weak transcription	Fetal Brain Female	brain
41	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:227370600-227379400	Weak transcription	NHDF-Ad	bronchial
43	chr1:227370600-227380000	Weak transcription	Gastric	stomach
44	chr1:227370800-227377800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:227370800-227378200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:227371400-227378600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:227371400-227381000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:227371600-227380000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:227371600-227381600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:227371800-227379400	Weak transcription	HSMM	muscle

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