Variant report

Variant	rs953504
Chromosome Location	chr13:97949389-97949390
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	chr13:97946659..97950744-chr13:97950983..97954750,4	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10508030	0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs10508031	0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs12864731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1328834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16951504	0.82[EUR][1000 genomes]
rs16954000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954002	0.82[EUR][1000 genomes]
rs17235614	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs17301362	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2389823	0.90[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap]
rs35039622	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35538229	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56940858	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57526148	0.82[EUR][1000 genomes]
rs58421118	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357402	0.82[EUR][1000 genomes]
rs61255793	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7999038	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9513227	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9513228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9513229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9513230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9513231	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9516891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9516895	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9584541	0.81[TSI][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	nsv1045777	chr13:97875574-97955134	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97914200-97960200	Weak transcription	Fetal Brain Male	brain
2	chr13:97925800-97987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr13:97929400-97955000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:97929600-97953400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr13:97929800-97953200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:97929800-97953400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:97931000-97953600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:97933000-97953600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr13:97933200-97949600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr13:97933200-97970400	Weak transcription	Placenta	Placenta
11	chr13:97933400-97952400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:97933600-97953600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr13:97934000-97954400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr13:97935600-97954800	Weak transcription	Colonic Mucosa	Colon
15	chr13:97935800-97949400	Weak transcription	Primary B cells from cord blood	blood
16	chr13:97936800-97949400	Weak transcription	Ovary	ovary
17	chr13:97936800-97949400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr13:97936800-97952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr13:97937000-97951400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr13:97939600-97949600	Weak transcription	Lung	lung
21	chr13:97941200-97950600	Weak transcription	Fetal Kidney	kidney
22	chr13:97942200-97950800	Weak transcription	Small Intestine	intestine
23	chr13:97942800-97995200	Weak transcription	Thymus	Thymus
24	chr13:97943400-97953600	Weak transcription	Esophagus	oesophagus
25	chr13:97943400-97957800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:97946400-97949400	Enhancers	Liver	Liver
27	chr13:97946400-97949600	Enhancers	HMEC	breast
28	chr13:97946400-97956400	Enhancers	Brain Cingulate Gyrus	brain
29	chr13:97946600-97949400	Enhancers	Brain Hippocampus Middle	brain
30	chr13:97946600-97949400	Enhancers	NH-A	brain
31	chr13:97946600-97949400	Enhancers	NHLF	lung
32	chr13:97946600-97951000	Enhancers	Brain Substantia Nigra	brain
33	chr13:97946600-97951600	Enhancers	Rectal Smooth Muscle	rectum
34	chr13:97946600-97956400	Enhancers	Brain Anterior Caudate	brain
35	chr13:97947000-97953200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr13:97947200-97949400	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr13:97947200-97949800	Enhancers	Osteobl	bone
38	chr13:97947400-97949400	Enhancers	Stomach Mucosa	stomach
39	chr13:97947400-97949400	Enhancers	Hela-S3	cervix
40	chr13:97947400-97954400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:97947600-97949600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr13:97947800-97949600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:97947800-97949800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr13:97947800-97950000	Enhancers	Fetal Intestine Large	intestine
45	chr13:97947800-97951000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:97947800-97953400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr13:97947800-97953600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr13:97948000-97949400	Weak transcription	Adipose Nuclei	Adipose
49	chr13:97948000-97949400	Weak transcription	Psoas Muscle	Psoas
50	chr13:97948000-97949400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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