Variant report

Variant	rs17112410
Chromosome Location	chr1:56050254-56050255
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1039295	1.00[EUR][1000 genomes]
rs10493193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10493194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10493196	0.91[YRI][hapmap]
rs11206626	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11206627	0.95[ASN][1000 genomes]
rs11206645	1.00[EUR][1000 genomes]
rs1165460	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12059018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068867	1.00[EUR][1000 genomes]
rs12071564	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12076746	1.00[EUR][1000 genomes]
rs12081733	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088041	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1392137	1.00[EUR][1000 genomes]
rs17112413	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28475680	1.00[EUR][1000 genomes]
rs59236443	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59539072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60149406	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6670673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6677373	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6680818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7416182	1.00[EUR][1000 genomes]
rs7520444	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7548272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:56042200-56052400	Weak transcription	Right Atrium	heart
3	chr1:56043000-56050400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:56044400-56051400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:56047000-56050400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:56047000-56050400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:56047000-56050400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:56047000-56050400	Weak transcription	Hela-S3	cervix
9	chr1:56047000-56051400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:56047400-56050400	Weak transcription	NH-A	brain
11	chr1:56048000-56050400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:56048200-56050400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:56048200-56050400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:56048400-56050400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:56048400-56050400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:56048400-56050400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:56048400-56050600	Weak transcription	HMEC	breast
18	chr1:56049400-56051200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:56049600-56051000	Enhancers	Fetal Muscle Trunk	muscle
20	chr1:56049600-56051200	Enhancers	Fetal Lung	lung
21	chr1:56049600-56051200	Enhancers	HSMM	muscle
22	chr1:56049600-56051400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:56049600-56051400	Enhancers	Fetal Stomach	stomach
24	chr1:56049600-56051600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:56049600-56051600	Enhancers	Fetal Muscle Leg	muscle
26	chr1:56049600-56052200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:56049600-56052400	Enhancers	Brain Germinal Matrix	brain
28	chr1:56049600-56053200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:56049800-56050600	Enhancers	Aorta	Aorta
30	chr1:56049800-56050600	Enhancers	Fetal Brain Male	brain
31	chr1:56049800-56050800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:56049800-56051200	Enhancers	Fetal Heart	heart
33	chr1:56049800-56051200	Enhancers	NHDF-Ad	bronchial
34	chr1:56049800-56051400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:56049800-56051400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:56049800-56051400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:56049800-56051400	Enhancers	Psoas Muscle	Psoas
38	chr1:56050000-56050600	Enhancers	Ovary	ovary
39	chr1:56050000-56051000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:56050000-56051200	Enhancers	Brain Hippocampus Middle	brain
41	chr1:56050000-56051200	Weak transcription	Spleen	Spleen
42	chr1:56050000-56051400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:56050000-56052600	Enhancers	Colon Smooth Muscle	Colon
44	chr1:56050200-56050800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:56050200-56051000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:56050200-56051200	Enhancers	Brain Anterior Caudate	brain
47	chr1:56050200-56051200	Enhancers	Osteobl	bone
48	chr1:56050200-56051400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:56050200-56051400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:56050200-56051400	Enhancers	NHLF	lung

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