Variant report

Variant	rs10489387
Chromosome Location	chr1:210540505-210540506
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	chr1:210500741..210504188-chr1:210538705..210542950,7	MCF-7	breast:
2	chr1:210501728..210505253-chr1:210538345..210542934,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054392	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11119480	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1883655	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2015743	0.81[JPT][hapmap]
rs2066721	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2103691	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2143590	0.81[ASN][1000 genomes]
rs2294844	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[EUR][1000 genomes]
rs2294847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765864	0.80[ASN][1000 genomes]
rs3765867	0.81[CEU][hapmap];0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs3765868	0.80[ASN][1000 genomes]
rs3765869	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3765873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765880	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819987	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4336853	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4844522	0.94[CEU][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs4845010	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[EUR][1000 genomes]
rs589027	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs590883	0.83[ASN][1000 genomes]
rs6540590	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6540591	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684767	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs761170	0.80[EUR][1000 genomes]
rs761172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs764585	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs910028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910033	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs9970232	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489387	HHAT	cis	cerebellum	SCAN

Chromatin state (count:48 , 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	chr1:210533200-210540800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:210534600-210541800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:210534600-210546800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:210534800-210543000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:210534800-210543000	Weak transcription	Right Atrium	heart
9	chr1:210536200-210542800	Weak transcription	HSMM	muscle
10	chr1:210536800-210551000	Weak transcription	Right Ventricle	heart
11	chr1:210536800-210558800	Weak transcription	Fetal Stomach	stomach
12	chr1:210537000-210550600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:210537800-210544600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:210538200-210542800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:210538400-210542600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:210538400-210547000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:210538400-210565600	Weak transcription	Esophagus	oesophagus
18	chr1:210538600-210546800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:210539200-210541000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:210539400-210541000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:210539600-210540600	Enhancers	Fetal Heart	heart
22	chr1:210539600-210541400	Enhancers	Brain Hippocampus Middle	brain
23	chr1:210539800-210541000	Enhancers	Brain Substantia Nigra	brain
24	chr1:210539800-210541200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:210539800-210541200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:210539800-210541600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:210540000-210540600	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:210540000-210540800	Enhancers	HSMMtube	muscle
29	chr1:210540000-210541000	Enhancers	Brain Angular Gyrus	brain
30	chr1:210540000-210541000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr1:210540000-210541000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr1:210540000-210541000	Enhancers	HMEC	breast
33	chr1:210540000-210541200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:210540000-210541200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr1:210540000-210541200	Enhancers	H9 Cell Line	embryonic stem cell
36	chr1:210540000-210541200	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:210540000-210541400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr1:210540000-210541800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr1:210540200-210540800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:210540200-210541000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:210540200-210541000	Enhancers	Brain Anterior Caudate	brain
42	chr1:210540200-210541200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:210540200-210541400	Enhancers	Fetal Brain Male	brain
44	chr1:210540400-210540600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:210540400-210540800	Enhancers	HepG2	liver
46	chr1:210540400-210541000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:210540400-210541200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr1:210540400-210541800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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