Variant report

Variant	rs1883655
Chromosome Location	chr1:210531438-210531439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210502542..210504337-chr1:210530347..210534050,4	MCF-7	breast:
2	chr1:210529252..210531698-chr1:210532960..210535588,2	MCF-7	breast:
3	chr1:210528590..210531540-chr1:210535112..210536681,2	MCF-7	breast:
4	chr1:210531383..210533438-chr1:210535536..210538131,3	K562	blood:

Variant related genes	Relation type
ENSG00000054392	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10489387	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]
rs11119480	0.85[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2015743	0.85[JPT][hapmap]
rs2103691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143590	0.87[ASN][1000 genomes]
rs2294844	0.83[CHB][hapmap]
rs2294847	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294848	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3765867	0.90[CHB][hapmap]
rs3765869	0.80[AMR][1000 genomes]
rs3765873	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3765880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819987	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4336853	0.90[CHB][hapmap]
rs4844522	0.80[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs4845010	0.80[CHB][hapmap]
rs589027	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs590883	0.89[ASN][1000 genomes]
rs642116	0.82[ASN][1000 genomes]
rs6540590	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540591	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs655213	0.85[ASN][1000 genomes]
rs684767	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs761172	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs764585	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs910028	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9970232	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[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
rs1883655	HHAT	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:210513000-210540400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210516800-210534400	Weak transcription	Fetal Lung	lung
4	chr1:210517000-210534400	Weak transcription	HSMM	muscle
5	chr1:210517200-210534400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:210517200-210534400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:210517200-210534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:210517200-210535800	Weak transcription	Right Ventricle	heart
9	chr1:210517200-210536000	Weak transcription	Fetal Stomach	stomach
10	chr1:210517200-210536000	Weak transcription	Left Ventricle	heart
11	chr1:210517400-210533200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:210517400-210534400	Weak transcription	Adipose Nuclei	Adipose
13	chr1:210517600-210536000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:210518600-210534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:210520800-210531800	Weak transcription	HSMMtube	muscle
16	chr1:210521000-210532000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:210521000-210534400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:210521200-210534400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:210521400-210534400	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:210522600-210537600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:210523000-210534400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:210525200-210538000	Weak transcription	Ovary	ovary
23	chr1:210526000-210534400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:210526200-210534600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:210527800-210534600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:210528400-210536600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:210528600-210531600	Weak transcription	Stomach Mucosa	stomach
28	chr1:210529400-210534400	Weak transcription	Brain Substantia Nigra	brain
29	chr1:210529600-210586000	Weak transcription	Pancreas	Pancrea
30	chr1:210531200-210531800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr1:210531200-210533400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr1:210531400-210531600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:210531400-210532000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr1:210531400-210532000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:210531400-210532400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:210531400-210532400	Enhancers	Fetal Heart	heart
37	chr1:210531400-210532600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr1:210531400-210532600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:210531400-210532800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:210531400-210532800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr1:210531400-210532800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:210531400-210532800	Enhancers	Brain Germinal Matrix	brain
43	chr1:210531400-210533000	Enhancers	H1 Cell Line	embryonic stem cell
44	chr1:210531400-210533200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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