Variant report

Variant	rs2947494
Chromosome Location	chr15:41375741-41375742
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41374877..41377715-chr15:41379772..41382441,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1009913	0.86[ASN][1000 genomes]
rs11853192	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11854472	0.97[ASN][1000 genomes]
rs11855248	0.80[ASN][1000 genomes]
rs11855797	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856572	0.90[ASN][1000 genomes]
rs11856577	0.86[ASN][1000 genomes]
rs11856848	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11858678	0.84[EUR][1000 genomes]
rs12101934	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12324159	0.85[EUR][1000 genomes]
rs12905926	0.80[ASN][1000 genomes]
rs12910027	0.80[ASN][1000 genomes]
rs1659227	0.84[EUR][1000 genomes]
rs1678750	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1717198	0.80[EUR][1000 genomes]
rs1717200	0.85[ASN][1000 genomes]
rs1962410	0.82[ASN][1000 genomes]
rs1983400	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2176998	0.91[ASN][1000 genomes]
rs2306083	0.90[ASN][1000 genomes]
rs2412601	0.89[ASN][1000 genomes]
rs2578655	0.85[EUR][1000 genomes]
rs28409432	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28455998	0.89[ASN][1000 genomes]
rs28501589	0.80[ASN][1000 genomes]
rs28510775	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28516683	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28581803	0.83[ASN][1000 genomes]
rs28613002	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28688742	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28729675	0.89[ASN][1000 genomes]
rs28828670	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28866311	0.86[ASN][1000 genomes]
rs2899013	0.83[EUR][1000 genomes]
rs2928148	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2928156	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2947493	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3100807	0.80[ASN][1000 genomes]
rs3101436	0.80[ASN][1000 genomes]
rs3101442	0.89[ASN][1000 genomes]
rs36046988	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4592624	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs476633	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs516156	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs537244	0.84[EUR][1000 genomes]
rs544744	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs551482	0.84[EUR][1000 genomes]
rs561301	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57393155	0.89[ASN][1000 genomes]
rs61203391	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492982	0.81[AFR][1000 genomes]
rs6492983	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492991	0.80[EUR][1000 genomes]
rs66818965	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs690733	0.84[EUR][1000 genomes]
rs691672	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs691702	0.84[EUR][1000 genomes]
rs691830	0.83[ASN][1000 genomes]
rs692153	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs692155	0.81[AFR][1000 genomes]
rs692195	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162992	0.80[ASN][1000 genomes]
rs7170049	0.83[EUR][1000 genomes]
rs7173841	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7179681	0.87[ASN][1000 genomes]
rs7180853	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7181816	0.97[ASN][1000 genomes]
rs8023345	0.85[ASN][1000 genomes]
rs8027932	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033435	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8037837	0.94[ASN][1000 genomes]
rs8042088	0.86[ASN][1000 genomes]
rs9888710	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9888718	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9972349	0.83[EUR][1000 genomes]
rs9972622	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053462	chr15:41270067-41396094	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2947494	CHP1	cis	Esophagus Mucosa	GTEx
rs2947494	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41328800-41388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:41334600-41389000	Strong transcription	Primary T helper cells PMA-I stimulated	--
3	chr15:41336800-41380400	Strong transcription	Osteobl	bone
4	chr15:41341600-41389000	Strong transcription	Liver	Liver
5	chr15:41347000-41380200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr15:41354200-41389200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:41354600-41388800	Strong transcription	Fetal Intestine Large	intestine
8	chr15:41354600-41389000	Strong transcription	Duodenum Mucosa	Duodenum
9	chr15:41354800-41388600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr15:41354800-41389200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:41355000-41380200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:41355000-41380800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:41355000-41381000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:41355000-41388400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:41355000-41389400	Strong transcription	Placenta	Placenta
16	chr15:41355000-41392000	Strong transcription	Fetal Thymus	thymus
17	chr15:41355000-41392400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:41355000-41393800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:41355200-41388600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:41355200-41388800	Strong transcription	Primary T cells from cord blood	blood
21	chr15:41355400-41378400	Strong transcription	Fetal Muscle Leg	muscle
22	chr15:41355400-41383200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:41355400-41388800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:41355400-41389200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:41355400-41390200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:41355400-41393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:41355600-41390800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:41355800-41381800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:41355800-41389200	Strong transcription	Dnd41	blood
30	chr15:41355800-41391000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:41356400-41388600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:41356600-41380000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:41356600-41387600	Strong transcription	Fetal Stomach	stomach
34	chr15:41356600-41388600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:41356600-41388600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:41356600-41389000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr15:41356800-41391000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:41356800-41392200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:41358000-41393600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr15:41358200-41392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:41359600-41388800	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:41359800-41381000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr15:41359800-41388600	Strong transcription	Fetal Brain Female	brain
44	chr15:41360200-41378400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:41360200-41378800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:41360400-41389200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:41361200-41407200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:41362800-41379000	Strong transcription	Fetal Intestine Small	intestine
49	chr15:41363600-41377000	Weak transcription	Psoas Muscle	Psoas
50	chr15:41363800-41388600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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