Variant report

Variant	rs2149971
Chromosome Location	chr13:30787214-30787215
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	chr13:30768141..30769932-chr13:30786883..30788704,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12585819	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12866391	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12870695	0.82[ASN][1000 genomes]
rs17632858	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs2031998	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2149970	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149973	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs28805029	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35331241	0.95[ASN][1000 genomes]
rs35963596	0.86[ASN][1000 genomes]
rs3803272	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3825532	0.91[CEU][hapmap];0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3825533	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7328946	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7987688	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9550538	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9550539	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9550540	0.81[ASN][1000 genomes]
rs9550541	0.81[ASN][1000 genomes]
rs9551867	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs9551868	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9551875	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9551879	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.89[AFR][1000 genomes];0.81[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	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30754000-30798800	Weak transcription	Brain Anterior Caudate	brain
2	chr13:30761600-30792800	Weak transcription	Fetal Brain Male	brain
3	chr13:30764600-30790200	Weak transcription	Colon Smooth Muscle	Colon
4	chr13:30765600-30807000	Weak transcription	Gastric	stomach
5	chr13:30766200-30790400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:30766400-30804400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr13:30768000-30795000	Weak transcription	Brain Germinal Matrix	brain
8	chr13:30768600-30792600	Weak transcription	Spleen	Spleen
9	chr13:30768600-30798800	Weak transcription	HMEC	breast
10	chr13:30769000-30796400	Weak transcription	A549	lung
11	chr13:30769800-30790400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:30770000-30790400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:30770000-30790400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:30770000-30799200	Weak transcription	HSMMtube	muscle
15	chr13:30770400-30790400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr13:30770600-30790400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:30770600-30796200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:30770600-30803200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr13:30771200-30790200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:30771200-30790400	Weak transcription	Right Ventricle	heart
21	chr13:30771800-30794800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr13:30772400-30796400	Weak transcription	NHEK	skin
23	chr13:30773400-30790400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr13:30774000-30796400	Weak transcription	Liver	Liver
25	chr13:30774200-30790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr13:30774200-30796000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr13:30774400-30812600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:30774600-30790400	Weak transcription	Aorta	Aorta
29	chr13:30774600-30790400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr13:30774600-30795800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr13:30774600-30802800	Weak transcription	Lung	lung
32	chr13:30774600-30805200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:30775000-30790600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr13:30775000-30803000	Weak transcription	Esophagus	oesophagus
35	chr13:30775600-30796600	Weak transcription	Fetal Kidney	kidney
36	chr13:30775800-30796600	Weak transcription	K562	blood
37	chr13:30776000-30790200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:30776000-30790400	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:30776200-30790400	Weak transcription	Left Ventricle	heart
40	chr13:30777000-30790200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr13:30777200-30796400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr13:30777200-30799000	Weak transcription	Brain Angular Gyrus	brain
43	chr13:30778000-30790600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr13:30779000-30790400	Weak transcription	Fetal Intestine Small	intestine
45	chr13:30779000-30795800	Weak transcription	Fetal Intestine Large	intestine
46	chr13:30779000-30796400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:30779400-30796400	Weak transcription	HepG2	liver
48	chr13:30779800-30795400	Weak transcription	Brain Substantia Nigra	brain
49	chr13:30779800-30796200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr13:30780000-30790400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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