Variant report

Variant	rs541896
Chromosome Location	chr1:169968420-169968421
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10494482	1.00[CHB][hapmap]
rs10919283	0.94[YRI][hapmap]
rs11584929	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589247	0.88[YRI][hapmap]
rs12089836	1.00[CHB][hapmap]
rs1330377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1541160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862745	0.88[YRI][hapmap]
rs16863058	1.00[CHB][hapmap]
rs2050628	0.94[YRI][hapmap]
rs2065950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2474708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28441321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527261	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs541655	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549002	0.84[AFR][1000 genomes]
rs571398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574053	1.00[CHB][hapmap]
rs614044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427230	0.94[YRI][hapmap]
rs6427232	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648576	0.80[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6668310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676005	1.00[CHB][hapmap]
rs6694304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs693673	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72715936	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7354853	1.00[CHB][hapmap]
rs7354854	1.00[CHB][hapmap]
rs7539241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9427175	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973015	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats 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 target site	37 gene(s)	inside rSNPs	diseases
2	nsv1012520	chr1:169899427-169969444	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1010370	chr1:169917450-169980951	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
2	chr1:169912000-169968600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:169914800-169984000	Weak transcription	Left Ventricle	heart
4	chr1:169914800-169984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:169914800-169988800	Weak transcription	Fetal Intestine Small	intestine
6	chr1:169922000-169984000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:169922400-169996400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:169944800-169989600	Weak transcription	Thymus	Thymus
9	chr1:169945800-169975000	Weak transcription	GM12878-XiMat	blood
10	chr1:169951600-170011800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:169951800-169975000	Weak transcription	Dnd41	blood
12	chr1:169951800-169975200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:169951800-169984800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:169952000-169983200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:169952000-169984600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:169952000-169985200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:169952000-170018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:169952200-169983000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:169952400-169983000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:169952400-169984600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:169952600-169975400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:169952600-169984800	Weak transcription	Fetal Intestine Large	intestine
24	chr1:169955000-169984800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:169955600-169984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:169956800-169997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:169960800-169970800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:169960800-169975000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:169966400-169968600	Weak transcription	Primary T cells from cord blood	blood
30	chr1:169966600-169984600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:169966800-169984600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:169966800-169984800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:169967200-169971400	Enhancers	NHDF-Ad	bronchial
34	chr1:169967200-169971600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:169967400-169969000	Enhancers	HSMM	muscle
36	chr1:169967400-169969400	Enhancers	Hela-S3	cervix
37	chr1:169967400-169969400	Enhancers	HMEC	breast
38	chr1:169967400-169969400	Enhancers	NHLF	lung
39	chr1:169967600-169969000	Enhancers	Fetal Lung	lung
40	chr1:169967600-169969400	Enhancers	Brain Germinal Matrix	brain
41	chr1:169967600-170013000	Weak transcription	Fetal Heart	heart
42	chr1:169967800-169968600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:169967800-169969600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:169968000-169968600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr1:169968000-169969000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:169968000-169969000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:169968000-169969000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:169968000-169969000	Enhancers	Brain Anterior Caudate	brain
49	chr1:169968000-169969000	Enhancers	Fetal Stomach	stomach
50	chr1:169968000-169969000	Enhancers	HUVEC	blood vessel

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