Variant report

Variant	rs6541386
Chromosome Location	chr1:94144417-94144418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94136961..94138617-chr1:94142462..94144751,2	K562	blood:
2	chr1:94144057..94145779-chr1:94248276..94250038,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1011903	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164962	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164963	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057736	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12079723	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084853	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12092517	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1567791	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236284	0.87[CEU][hapmap]
rs236287	0.87[CEU][hapmap]
rs236344	0.80[MEX][hapmap]
rs423493	0.80[MEX][hapmap]
rs61781002	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541387	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541388	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6657709	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6660740	1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6701871	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6702036	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704479	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7513130	0.85[CEU][hapmap]
rs7519952	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs955470	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9659100	0.84[EUR][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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94129200-94144800	Weak transcription	GM12878-XiMat	blood
2	chr1:94132800-94144600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:94136000-94144800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:94138200-94145000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:94138600-94145200	Weak transcription	Gastric	stomach
6	chr1:94138600-94145800	Weak transcription	Colonic Mucosa	Colon
7	chr1:94138600-94145800	Weak transcription	Fetal Stomach	stomach
8	chr1:94139000-94145200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:94139200-94144800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:94139200-94145200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:94139200-94146000	Weak transcription	Liver	Liver
12	chr1:94139600-94145600	Weak transcription	Stomach Mucosa	stomach
13	chr1:94140200-94146200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:94140400-94145800	Weak transcription	Esophagus	oesophagus
15	chr1:94140600-94144800	Enhancers	NHDF-Ad	bronchial
16	chr1:94141000-94146200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:94141200-94144600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:94141200-94144800	Enhancers	Brain Anterior Caudate	brain
19	chr1:94141200-94146000	Weak transcription	Brain Angular Gyrus	brain
20	chr1:94141400-94145800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:94141400-94146200	Weak transcription	Aorta	Aorta
22	chr1:94141600-94145000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:94141800-94145200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:94141800-94145600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:94142000-94145000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:94142200-94145200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:94142200-94145800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:94142400-94144800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:94142400-94145200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:94142400-94145200	Weak transcription	Ovary	ovary
31	chr1:94142400-94145400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:94142400-94145800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:94142400-94145800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:94142400-94145800	Weak transcription	Primary B cells from cord blood	blood
35	chr1:94142400-94145800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:94142400-94146000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:94142400-94146000	Weak transcription	Pancreas	Pancrea
38	chr1:94142600-94144800	Weak transcription	Fetal Lung	lung
39	chr1:94142600-94145800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:94143000-94144800	Weak transcription	HSMMtube	muscle
41	chr1:94143000-94146000	Weak transcription	Spleen	Spleen
42	chr1:94143200-94144800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:94143200-94145000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:94143200-94145200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:94143200-94145200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:94143200-94145800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:94143200-94145800	Weak transcription	Right Ventricle	heart
48	chr1:94143200-94145800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:94143400-94144600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:94143400-94144800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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