Variant report

Variant	rs41446844
Chromosome Location	chr1:57031938-57031939
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	chr1:57015989..57018935-chr1:57031658..57034048,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10888981	0.80[AFR][1000 genomes]
rs11206845	0.95[AFR][1000 genomes]
rs11206846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800865	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11800883	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810635	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12058536	0.95[AFR][1000 genomes]
rs12059747	1.00[ASW][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs12059843	0.95[AFR][1000 genomes]
rs12070247	1.00[ASW][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs12070557	0.95[AFR][1000 genomes]
rs12090895	0.95[AFR][1000 genomes]
rs12098117	0.94[YRI][hapmap];0.95[AFR][1000 genomes]
rs1418521	1.00[CEU][hapmap];0.81[MKK][hapmap];0.81[YRI][hapmap]
rs1572058	0.90[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114100	1.00[CEU][hapmap]
rs17114110	1.00[CEU][hapmap]
rs17114113	1.00[CEU][hapmap]
rs17114115	1.00[CEU][hapmap]
rs17114126	1.00[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs17114127	1.00[CEU][hapmap]
rs28673510	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56332336	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6661359	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699960	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6702052	0.95[AFR][1000 genomes]
rs72664373	0.96[ASN][1000 genomes]
rs72664400	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72903425	0.95[AFR][1000 genomes]
rs7539051	0.90[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57016000-57038600	Weak transcription	HSMMtube	muscle
2	chr1:57017400-57035400	Weak transcription	Esophagus	oesophagus
3	chr1:57017400-57035400	Weak transcription	Fetal Thymus	thymus
4	chr1:57017400-57039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:57017800-57040800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:57021400-57032800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:57023800-57033000	Enhancers	Brain Hippocampus Middle	brain
8	chr1:57025600-57040000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:57026000-57033200	Enhancers	Fetal Intestine Large	intestine
10	chr1:57026200-57032200	Enhancers	Ovary	ovary
11	chr1:57026200-57033000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:57026800-57033000	Enhancers	Fetal Intestine Small	intestine
13	chr1:57027000-57034200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:57027400-57032000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:57027400-57034200	Enhancers	Brain Anterior Caudate	brain
16	chr1:57027400-57034400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:57027600-57032800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:57027600-57033000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:57027800-57032400	Enhancers	H9 Cell Line	embryonic stem cell
20	chr1:57027800-57032800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr1:57027800-57033000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr1:57027800-57033200	Enhancers	Brain Cingulate Gyrus	brain
23	chr1:57027800-57034400	Enhancers	Brain Substantia Nigra	brain
24	chr1:57028000-57032600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:57028000-57033000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:57028000-57035400	Weak transcription	Colonic Mucosa	Colon
27	chr1:57028200-57032800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:57028200-57032800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:57028200-57033000	Enhancers	Brain Angular Gyrus	brain
30	chr1:57028400-57032600	Enhancers	Adipose Nuclei	Adipose
31	chr1:57028400-57033000	Enhancers	Duodenum Mucosa	Duodenum
32	chr1:57028600-57033000	Enhancers	Colon Smooth Muscle	Colon
33	chr1:57028800-57034400	Weak transcription	Lung	lung
34	chr1:57028800-57035400	Weak transcription	Gastric	stomach
35	chr1:57029000-57032400	Enhancers	Left Ventricle	heart
36	chr1:57029200-57032200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:57029200-57032800	Weak transcription	Fetal Brain Male	brain
38	chr1:57029400-57032800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:57029400-57042200	Weak transcription	Thymus	Thymus
40	chr1:57029800-57032000	Enhancers	Fetal Stomach	stomach
41	chr1:57030000-57032200	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr1:57030000-57035400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:57030200-57032200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:57030200-57032200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:57030400-57032200	Genic enhancers	HSMM	muscle
46	chr1:57030400-57033000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:57030600-57032400	Genic enhancers	Fetal Muscle Leg	muscle
48	chr1:57030600-57032400	Enhancers	Right Ventricle	heart
49	chr1:57030600-57032800	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr1:57030600-57033000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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