Variant report

Variant	rs2649903
Chromosome Location	chr12:123244859-123244860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123242966..123245804-chr12:123255360..123258267,2	MCF-7	breast:
2	chr12:123240856..123246035-chr12:123255741..123259598,6	MCF-7	breast:
3	chr12:123237435..123239674-chr12:123244773..123246396,2	K562	blood:
4	chr12:123235825..123239582-chr12:123243364..123250296,6	MCF-7	breast:
5	chr12:123235308..123239495-chr12:123239510..123247125,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139726	Chromatin interaction
ENSG00000130783	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10773599	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847742	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847749	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847751	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847775	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10847910	1.00[JPT][hapmap]
rs10848148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11059729	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11060152	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11060932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11060999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12311043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1260121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671684	1.00[JPT][hapmap]
rs1671687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1696355	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649894	0.87[ASN][1000 genomes]
rs2649895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649900	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649914	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844369	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4307760	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs548349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489241	1.00[CEU][hapmap]
rs651683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs7485652	1.00[JPT][hapmap]
rs7957643	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[JPT][hapmap]
rs839352	0.83[AMR][1000 genomes]
rs839354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839355	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839357	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs839362	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897386	0.82[CEU][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9795629	1.00[CEU][hapmap];1.00[JPT][hapmap]

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	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123238200-123249400	Weak transcription	Aorta	Aorta
2	chr12:123238400-123258000	Strong transcription	Fetal Muscle Trunk	muscle
3	chr12:123238600-123245200	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:123238600-123248400	Weak transcription	Right Ventricle	heart
5	chr12:123238600-123249000	Weak transcription	Fetal Heart	heart
6	chr12:123238600-123250800	Weak transcription	Stomach Mucosa	stomach
7	chr12:123238600-123255600	Strong transcription	Fetal Intestine Large	intestine
8	chr12:123238600-123255800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr12:123238600-123258800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:123238800-123245000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:123238800-123245200	Strong transcription	Fetal Lung	lung
12	chr12:123238800-123245400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:123238800-123245400	Weak transcription	Esophagus	oesophagus
14	chr12:123238800-123245600	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr12:123238800-123245600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:123238800-123246000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:123238800-123246000	Weak transcription	Pancreas	Pancrea
18	chr12:123238800-123246200	Strong transcription	Brain Cingulate Gyrus	brain
19	chr12:123238800-123246400	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:123238800-123246600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:123238800-123255600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:123238800-123255600	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:123238800-123255800	Strong transcription	Primary B cells from cord blood	blood
24	chr12:123238800-123255800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:123238800-123255800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:123238800-123255800	Strong transcription	Liver	Liver
27	chr12:123238800-123256000	Strong transcription	NH-A	brain
28	chr12:123238800-123256200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:123238800-123256200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:123238800-123256200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:123238800-123256200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:123238800-123256600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr12:123238800-123257400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:123238800-123257400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:123238800-123257600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:123238800-123257800	Strong transcription	Fetal Thymus	thymus
37	chr12:123238800-123257800	Strong transcription	Osteobl	bone
38	chr12:123238800-123258000	Strong transcription	Placenta	Placenta
39	chr12:123239000-123245000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:123239000-123245200	Strong transcription	HSMM	muscle
41	chr12:123239000-123245600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:123239000-123246400	Strong transcription	Primary T cells from cord blood	blood
43	chr12:123239000-123252600	Strong transcription	NHDF-Ad	bronchial
44	chr12:123239000-123255200	Strong transcription	Brain Hippocampus Middle	brain
45	chr12:123239000-123255600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr12:123239000-123255600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr12:123239000-123255600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr12:123239000-123256600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:123239000-123257400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:123239000-123257600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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