Variant report

Variant	rs10489386
Chromosome Location	chr1:210541178-210541179
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210534514..210536655-chr1:210541049..210542825,2	K562	blood:
2	chr1:210540564..210542647-chr1:210551469..210554049,2	MCF-7	breast:
3	chr1:210500741..210504188-chr1:210538705..210542950,7	MCF-7	breast:
4	chr1:210501728..210505253-chr1:210538345..210542934,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054392	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1005174	1.00[AFR][1000 genomes]
rs10489383	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10489385	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10863819	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10863820	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10863822	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863825	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11119458	1.00[AFR][1000 genomes]
rs11119462	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11119473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119475	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119485	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12024862	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12030512	0.86[AFR][1000 genomes]
rs12030856	0.86[AFR][1000 genomes]
rs12034871	0.86[AFR][1000 genomes]
rs12040684	0.86[AFR][1000 genomes]
rs12046133	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12049137	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12062126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12087955	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120970	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12141780	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12143463	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1338288	0.85[EUR][1000 genomes]
rs1338289	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17016002	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2143591	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2294843	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2294851	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2357435	0.83[EUR][1000 genomes]
rs2357584	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2884218	0.80[ASN][1000 genomes]
rs3753230	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3765856	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3765865	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3765866	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3765877	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765878	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3765886	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4844520	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4844996	0.86[AFR][1000 genomes]
rs4844997	1.00[AFR][1000 genomes]
rs58469250	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58960429	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60154123	0.86[AFR][1000 genomes]
rs7525927	1.00[AFR][1000 genomes]
rs7550576	0.88[AMR][1000 genomes];0.82[EUR][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	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
3	chr1:210532400-210545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:210534600-210541800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:210534600-210546800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:210534800-210543000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:210534800-210543000	Weak transcription	Right Atrium	heart
8	chr1:210536200-210542800	Weak transcription	HSMM	muscle
9	chr1:210536800-210551000	Weak transcription	Right Ventricle	heart
10	chr1:210536800-210558800	Weak transcription	Fetal Stomach	stomach
11	chr1:210537000-210550600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:210537800-210544600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:210538200-210542800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:210538400-210542600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:210538400-210547000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:210538400-210565600	Weak transcription	Esophagus	oesophagus
17	chr1:210538600-210546800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:210539600-210541400	Enhancers	Brain Hippocampus Middle	brain
19	chr1:210539800-210541200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:210539800-210541200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:210539800-210541600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:210540000-210541200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:210540000-210541200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:210540000-210541200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr1:210540000-210541200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr1:210540000-210541400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr1:210540000-210541800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:210540200-210541200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:210540200-210541400	Enhancers	Fetal Brain Male	brain
30	chr1:210540400-210541200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:210540400-210541800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:210540600-210541200	Enhancers	Fetal Brain Female	brain
33	chr1:210540600-210542800	Weak transcription	Fetal Heart	heart
34	chr1:210540600-210543200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:210540800-210541200	Flanking Active TSS	HepG2	liver
36	chr1:210540800-210541400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:210540800-210541800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr1:210540800-210549600	Weak transcription	HSMMtube	muscle
39	chr1:210541000-210543200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:210541000-210545000	Weak transcription	HMEC	breast
41	chr1:210541000-210545400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:210541000-210546000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:210541000-210550000	Weak transcription	Brain Anterior Caudate	brain

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