Variant report

Variant	rs4420508
Chromosome Location	chr15:40956681-40956682
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40954350..40957294-chr15:40985826..40987543,2	K562	blood:

Variant related genes	Relation type
ENSG00000245849	Chromatin interaction
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10400825	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10467972	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10744948	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070284	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070285	0.80[JPT][hapmap]
rs11070286	0.80[JPT][hapmap]
rs11070292	0.91[CEU][hapmap]
rs1142468	0.84[EUR][1000 genomes]
rs11561564	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11629680	0.83[EUR][1000 genomes]
rs11632370	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs11633367	0.83[EUR][1000 genomes]
rs11638204	0.89[EUR][1000 genomes]
rs11852694	0.81[JPT][hapmap]
rs11854763	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11854986	0.81[JPT][hapmap]
rs11855334	0.80[JPT][hapmap]
rs11855923	0.81[JPT][hapmap]
rs11856438	0.81[JPT][hapmap]
rs11856802	0.81[JPT][hapmap]
rs11858113	0.80[JPT][hapmap]
rs12438955	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12440468	0.85[EUR][1000 genomes]
rs12592882	0.87[EUR][1000 genomes]
rs12708401	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12899600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905162	0.81[JPT][hapmap]
rs12906095	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12911738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912339	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12914743	0.81[JPT][hapmap]
rs12915109	0.89[EUR][1000 genomes]
rs12916082	0.89[EUR][1000 genomes]
rs16970851	0.80[JPT][hapmap]
rs17747351	1.00[CEU][hapmap]
rs1901775	0.87[EUR][1000 genomes]
rs2278888	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes]
rs2304580	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[EUR][1000 genomes]
rs2412531	0.80[JPT][hapmap];0.86[YRI][hapmap]
rs2412532	0.82[JPT][hapmap];0.84[YRI][hapmap]
rs2412541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412544	0.80[JPT][hapmap]
rs2619681	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2924388	0.81[JPT][hapmap]
rs3092978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3092979	0.81[JPT][hapmap]
rs34285050	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35047458	0.80[JPT][hapmap]
rs3751653	0.80[JPT][hapmap]
rs4306472	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4417527	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4439732	0.85[EUR][1000 genomes]
rs45457497	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4923876	0.80[JPT][hapmap];0.86[YRI][hapmap]
rs4924478	0.80[JPT][hapmap]
rs4924481	0.80[JPT][hapmap]
rs4924484	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924487	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924490	0.83[EUR][1000 genomes]
rs4924491	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924500	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55640412	0.85[EUR][1000 genomes]
rs62019923	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62019924	0.87[AMR][1000 genomes]
rs62019925	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6492957	0.92[EUR][1000 genomes]
rs6492958	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs66885559	0.86[EUR][1000 genomes]
rs7161938	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7161968	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7162319	0.84[EUR][1000 genomes]
rs7162509	0.86[EUR][1000 genomes]
rs7164289	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7167417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7167768	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7168873	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7171945	0.85[EUR][1000 genomes]
rs7172947	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7175361	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176221	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176974	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7177192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178486	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025008	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8026605	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs8028999	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs8029384	0.81[JPT][hapmap]
rs8031057	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8035775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8037417	0.84[EUR][1000 genomes]
rs8037804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8041095	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8041443	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042729	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs896795	0.80[JPT][hapmap]
rs896796	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs936580	0.95[EUR][1000 genomes]
rs9806221	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40913800-40986000	Weak transcription	A549	lung
4	chr15:40914400-40960000	Weak transcription	NHLF	lung
5	chr15:40919200-40957600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:40919400-40956800	Strong transcription	Fetal Thymus	thymus
7	chr15:40926000-40958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:40928600-40958000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:40939800-40956800	Strong transcription	Dnd41	blood
10	chr15:40939800-40956800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:40941400-40957600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:40942000-40959000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:40943000-40971400	Weak transcription	Primary B cells from cord blood	blood
14	chr15:40945000-40984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:40945200-40961400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:40946600-40957600	Weak transcription	HSMM	muscle
17	chr15:40946600-40957600	Weak transcription	NH-A	brain
18	chr15:40946600-40959800	Weak transcription	Gastric	stomach
19	chr15:40949200-40957400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:40950000-40958600	Weak transcription	HUVEC	blood vessel
21	chr15:40950000-40958800	Weak transcription	HepG2	liver
22	chr15:40950000-40981200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:40950200-40964200	Weak transcription	Osteobl	bone
24	chr15:40951800-40957800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:40953000-40956800	Strong transcription	Hela-S3	cervix
26	chr15:40953000-40960200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:40953400-40957200	Weak transcription	K562	blood
28	chr15:40953800-40957400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr15:40953800-40960000	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:40954600-40959800	Weak transcription	NHEK	skin
31	chr15:40954800-40958200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:40954800-40958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:40954800-40959600	Weak transcription	Liver	Liver
34	chr15:40954800-40960000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:40955000-40957600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:40955000-40958600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:40955200-40956800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:40955200-40956800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:40955200-40956800	Weak transcription	Fetal Intestine Large	intestine
40	chr15:40955200-40957600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:40955200-40958000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr15:40955200-40958200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:40955200-40958200	Weak transcription	Thymus	Thymus
44	chr15:40955200-40959800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:40955200-40961000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:40955200-40964400	Weak transcription	GM12878-XiMat	blood
47	chr15:40955200-40976600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:40955200-40983200	Weak transcription	Fetal Intestine Small	intestine
49	chr15:40955400-40960400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:40955600-40959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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