Variant report

Variant	rs10399817
Chromosome Location	chr1:184430752-184430753
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184412654..184414882-chr1:184428797..184431309,2	MCF-7	breast:
2	chr1:184429671..184432533-chr1:184459614..184461411,2	K562	blood:
3	chr1:184353853..184357203-chr1:184430668..184434777,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116667	Chromatin interaction
ENSG00000271387	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10911610	0.89[CHB][hapmap]
rs12117823	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs12120604	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12121612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127697	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs12129904	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12138103	0.93[CHB][hapmap];0.93[ASN][1000 genomes]
rs1535132	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1535135	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs16823195	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs16823197	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs16823238	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2207526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207527	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs58231072	0.95[ASN][1000 genomes]
rs6659261	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs6683932	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs6693408	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs7513091	0.94[CHB][hapmap];0.82[GIH][hapmap]
rs7525267	0.90[ASN][1000 genomes]
rs7548188	0.92[ASN][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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184419200-184438400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:184419600-184432600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:184421400-184433000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr1:184423000-184431200	Weak transcription	Fetal Intestine Small	intestine
5	chr1:184424000-184436400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:184425400-184442200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:184427000-184431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:184427400-184431200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:184427400-184431200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:184427400-184443800	Weak transcription	Esophagus	oesophagus
11	chr1:184427400-184444000	Weak transcription	Lung	lung
12	chr1:184427400-184448400	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:184428600-184431600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:184428800-184430800	Enhancers	Left Ventricle	heart
15	chr1:184429000-184454800	Weak transcription	Aorta	Aorta
16	chr1:184429200-184431000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:184429200-184431000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:184429200-184431400	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:184429400-184431400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:184429400-184432800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:184429400-184432800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:184429400-184434800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:184429400-184449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:184429600-184434600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:184429600-184442200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:184429800-184430800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:184429800-184430800	Enhancers	Psoas Muscle	Psoas
28	chr1:184429800-184436600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:184430000-184431000	Enhancers	Ovary	ovary
30	chr1:184430000-184431400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:184430000-184431400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:184430000-184431400	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:184430000-184431800	Enhancers	Adipose Nuclei	Adipose
34	chr1:184430200-184430800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:184430200-184430800	Enhancers	Fetal Intestine Large	intestine
36	chr1:184430200-184431000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:184430200-184431200	Enhancers	Fetal Lung	lung
38	chr1:184430200-184431600	Enhancers	NHLF	lung
39	chr1:184430200-184431800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:184430200-184431800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:184430400-184431400	Weak transcription	Spleen	Spleen
42	chr1:184430400-184431800	Enhancers	Fetal Heart	heart
43	chr1:184430400-184439000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:184430600-184431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:184430600-184431600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr1:184430600-184431600	Enhancers	NHEK	skin
47	chr1:184430600-184433800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:184430600-184434600	Weak transcription	Right Atrium	heart
49	chr1:184430600-184436400	Weak transcription	Pancreas	Pancrea
50	chr1:184430600-184444000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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