Variant report

Variant	rs6426494
Chromosome Location	chr1:228437603-228437604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10737429	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916276	0.82[AMR][1000 genomes]
rs10916278	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10916292	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916293	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1188704	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1188721	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1188722	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1188724	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12022917	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12026358	0.82[AMR][1000 genomes]
rs12047879	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12142165	0.82[AMR][1000 genomes]
rs12741048	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12755546	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1411912	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411915	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757130	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771455	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1771456	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1771457	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1888680	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888681	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2150669	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2487384	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs287613	0.85[EUR][1000 genomes]
rs3795780	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4085473	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs450088	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4653932	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533738	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6426493	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6426495	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426496	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6665929	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668967	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6677503	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517088	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517108	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526808	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529241	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532144	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535667	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878388	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936885	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs947084	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
9	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv873263	chr1:228391808-228494790	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv873264	chr1:228423647-228543800	Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv520340	chr1:228423936-228456147	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv873265	chr1:228434395-228525008	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv873266	chr1:228434395-228537942	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases
15	nsv873267	chr1:228434395-228585837	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228429000-228439400	Strong transcription	HSMMtube	muscle
2	chr1:228430600-228447000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:228430800-228440000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:228431200-228439800	Strong transcription	Left Ventricle	heart
5	chr1:228433200-228442400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:228433400-228449400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:228433600-228438000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:228433600-228438400	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr1:228434000-228439600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:228434200-228438600	Strong transcription	Fetal Lung	lung
11	chr1:228434400-228440200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:228434400-228440400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:228434400-228441600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:228434600-228439800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:228434600-228439800	Weak transcription	Right Atrium	heart
16	chr1:228434600-228440200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:228434600-228440200	Strong transcription	Fetal Thymus	thymus
18	chr1:228434600-228440600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:228434600-228444400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:228434600-228455400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:228434800-228438400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:228434800-228439200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:228434800-228440600	Strong transcription	Fetal Stomach	stomach
24	chr1:228434800-228444000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:228434800-228444000	Weak transcription	Ovary	ovary
26	chr1:228434800-228444600	Strong transcription	Dnd41	blood
27	chr1:228434800-228445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:228434800-228460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:228434800-228462400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:228435000-228440400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:228435000-228441000	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:228435000-228441200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:228435000-228441200	Weak transcription	Fetal Brain Male	brain
34	chr1:228435000-228442400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:228435000-228442800	Weak transcription	Aorta	Aorta
36	chr1:228435000-228444000	Weak transcription	Esophagus	oesophagus
37	chr1:228435000-228446000	Weak transcription	A549	lung
38	chr1:228435200-228438200	Weak transcription	NHEK	skin
39	chr1:228435200-228440400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:228435200-228440400	Strong transcription	Thymus	Thymus
41	chr1:228435200-228443200	Weak transcription	Fetal Kidney	kidney
42	chr1:228435200-228449400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:228435200-228449600	Strong transcription	Primary T cells from cord blood	blood
44	chr1:228435200-228462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:228435400-228438800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:228435400-228441800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:228435600-228439000	Weak transcription	Brain Germinal Matrix	brain
48	chr1:228435600-228462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:228435800-228440000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:228435800-228446400	Weak transcription	Fetal Heart	heart

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