Variant report

Variant	rs9534944
Chromosome Location	chr13:48643773-48643774
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	chr13:48641348..48644169-chr13:48669031..48670596,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136146	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11616639	0.86[ASN][1000 genomes]
rs1410117	0.93[ASN][1000 genomes]
rs1571256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1927213	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2094192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104480	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2148246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2148938	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2406709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406797	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4294712	0.93[ASN][1000 genomes]
rs4369555	1.00[JPT][hapmap]
rs4941623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4942712	0.84[JPT][hapmap]
rs4942748	0.97[ASN][1000 genomes]
rs56399021	0.93[ASN][1000 genomes]
rs7324484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326363	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7333247	0.85[ASN][1000 genomes]
rs7336214	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8001243	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9526407	0.89[JPT][hapmap]
rs9526442	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9526443	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9526445	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526447	0.93[ASN][1000 genomes]
rs9526449	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526451	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534856	0.84[JPT][hapmap]
rs9534857	0.84[JPT][hapmap]
rs9534888	1.00[JPT][hapmap]
rs9534931	0.84[ASN][1000 genomes]
rs9534932	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534933	0.92[ASN][1000 genomes]
rs9534937	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9534939	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9534943	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534945	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534946	0.94[ASN][1000 genomes]
rs9534947	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9534948	0.94[ASN][1000 genomes]
rs9534949	0.89[ASN][1000 genomes]
rs9534950	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9534951	0.90[ASN][1000 genomes]
rs9534952	0.93[ASN][1000 genomes]
rs9534957	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9534961	0.84[ASN][1000 genomes]
rs9534965	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9562802	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567987	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9567991	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9567994	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9568000	0.87[ASN][1000 genomes]
rs9568014	0.86[CHB][hapmap]

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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
2	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr13:48613600-48645000	Weak transcription	Small Intestine	intestine
4	chr13:48618800-48644800	Weak transcription	Colonic Mucosa	Colon
5	chr13:48623200-48652200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr13:48627400-48644800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr13:48627400-48645000	Weak transcription	Gastric	stomach
8	chr13:48627400-48645200	Weak transcription	Aorta	Aorta
9	chr13:48627800-48644200	Weak transcription	Spleen	Spleen
10	chr13:48628400-48644200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr13:48634600-48644800	Weak transcription	Right Ventricle	heart
12	chr13:48636600-48651400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr13:48636600-48655400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr13:48638200-48650000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr13:48638800-48651400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr13:48638800-48651600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr13:48639000-48648800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:48639400-48648600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
19	chr13:48639600-48643800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:48639600-48649800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr13:48639800-48644200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr13:48640000-48648600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr13:48640000-48649800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr13:48640200-48643800	Strong transcription	Osteobl	bone
25	chr13:48640200-48644200	Strong transcription	NH-A	brain
26	chr13:48640200-48646600	ZNF genes & repeats	Adipose Nuclei	Adipose
27	chr13:48640200-48647000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
28	chr13:48640200-48648600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:48640200-48648600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
30	chr13:48640200-48648600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:48640200-48648600	ZNF genes & repeats	Fetal Brain Female	brain
32	chr13:48640200-48648600	ZNF genes & repeats	Fetal Lung	lung
33	chr13:48640200-48648600	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr13:48640200-48649800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:48640200-48649800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr13:48640200-48649800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr13:48640200-48661200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr13:48640400-48644200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:48640400-48645000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr13:48640400-48648200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr13:48640400-48648600	ZNF genes & repeats	Liver	Liver
42	chr13:48640400-48655600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr13:48640600-48643800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr13:48640600-48648400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:48640800-48647000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:48640800-48648200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr13:48640800-48648600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr13:48641000-48645000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:48641000-48645200	Weak transcription	Pancreas	Pancrea
50	chr13:48641200-48647400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin

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