Variant report

Variant	rs2664126
Chromosome Location	chr15:39985085-39985086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39984467..39987996-chr15:40003626..40006912,3	K562	blood:
2	chr15:39984161..39987304-chr15:39989320..39992486,3	K562	blood:
3	chr15:39980861..39985158-chr15:39988045..39992700,5	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070231	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11854306	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11855578	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1320036	0.91[ASN][1000 genomes]
rs1906153	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1906159	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1906160	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2087133	0.87[ASN][1000 genomes]
rs2129458	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2171310	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2254829	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2254942	0.94[ASN][1000 genomes]
rs2254947	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2412424	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2412426	0.81[JPT][hapmap]
rs2631692	0.95[ASN][1000 genomes]
rs2631693	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2631694	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2631695	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631696	0.94[ASN][1000 genomes]
rs2631698	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631702	0.85[CEU][hapmap]
rs2631703	0.91[ASN][1000 genomes]
rs2631705	0.85[CEU][hapmap]
rs2631708	0.93[ASN][1000 genomes]
rs2631709	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2631711	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631712	0.94[ASN][1000 genomes]
rs2631713	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2631715	0.94[ASN][1000 genomes]
rs2664124	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2664127	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2664129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2664130	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2664131	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2664132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3103065	0.83[CEU][hapmap]
rs3103066	0.95[ASN][1000 genomes]
rs4429263	0.85[CEU][hapmap]
rs4924380	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs62004771	0.90[ASN][1000 genomes]
rs62004772	0.95[ASN][1000 genomes]
rs67426899	0.90[ASN][1000 genomes]
rs7171939	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028503	0.94[ASN][1000 genomes]
rs8035895	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39977200-39990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:39982000-39985800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr15:39982600-39985800	Enhancers	Fetal Stomach	stomach
4	chr15:39982800-39985200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:39982800-39986200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:39982800-39986400	Enhancers	Brain Germinal Matrix	brain
7	chr15:39983000-39985800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:39983000-39989800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:39983200-39985400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:39983200-39985800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr15:39983200-39990800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:39983400-39985800	Enhancers	Fetal Brain Male	brain
13	chr15:39983600-39986200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:39983800-39985400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:39983800-39985800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr15:39983800-39987200	Weak transcription	K562	blood
17	chr15:39984200-39985600	Enhancers	Brain Anterior Caudate	brain
18	chr15:39984200-39986200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:39984400-39985400	Enhancers	Fetal Kidney	kidney
20	chr15:39984400-39985600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr15:39984400-39985600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr15:39984600-39985400	Enhancers	Brain Cingulate Gyrus	brain
23	chr15:39984600-39985600	Enhancers	Brain Angular Gyrus	brain
24	chr15:39984600-39985800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr15:39984800-39985600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr15:39984800-39986200	Enhancers	Fetal Intestine Large	intestine
27	chr15:39985000-39985200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:39985000-39985200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr15:39985000-39985200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:39985000-39985200	Flanking Active TSS	Fetal Brain Female	brain
31	chr15:39985000-39985200	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr15:39985000-39985400	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr15:39985000-39985400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr15:39985000-39985400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr15:39985000-39985400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:39985000-39985400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:39985000-39985400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:39985000-39985400	Active TSS	Brain Hippocampus Middle	brain
39	chr15:39985000-39985400	Active TSS	Colon Smooth Muscle	Colon
40	chr15:39985000-39985400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr15:39985000-39985400	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr15:39985000-39985400	Active TSS	Ovary	ovary
43	chr15:39985000-39985400	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr15:39985000-39985400	Active TSS	NHDF-Ad	bronchial
45	chr15:39985000-39985600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:39985000-39985600	Flanking Active TSS	Fetal Lung	lung
47	chr15:39985000-39985600	Enhancers	Fetal Muscle Leg	muscle
48	chr15:39985000-39985800	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr15:39985000-39985800	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr15:39985000-39985800	Enhancers	NHEK	skin

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