Variant report

Variant	rs4815445
Chromosome Location	chr20:25675602-25675603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25675586..25677215-chr20:25728197..25729782,2	MCF-7	breast:
2	chr20:25673244..25674804-chr20:25675051..25677255,2	K562	blood:
3	chr20:25604068..25607059-chr20:25675582..25678596,4	MCF-7	breast:
4	chr20:25602422..25607796-chr20:25675112..25679388,9	K562	blood:
5	chr20:25666393..25667340-chr20:25675280..25676053,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170191	Chromatin interaction
ENSG00000213742	Chromatin interaction

Extended variants
information (count: 175 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:172)

rs_ID	r²[population]
rs10485776	1.00[JPT][hapmap]
rs1109100	1.00[JPT][hapmap]
rs1122769	1.00[JPT][hapmap]
rs12106173	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1569617	1.00[JPT][hapmap]
rs16987789	1.00[JPT][hapmap]
rs16987799	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs16987820	1.00[JPT][hapmap]
rs16987934	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16988014	1.00[JPT][hapmap]
rs1883528	1.00[JPT][hapmap]
rs2103661	0.85[JPT][hapmap]
rs2179458	1.00[JPT][hapmap]
rs2387977	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2388026	0.86[ASN][1000 genomes]
rs242130	0.90[CHD][hapmap]
rs242133	1.00[JPT][hapmap]
rs35516971	0.81[ASN][1000 genomes]
rs3764695	0.86[ASN][1000 genomes]
rs3813916	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs402120	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4098823	0.86[ASN][1000 genomes]
rs4098824	0.86[ASN][1000 genomes]
rs4113658	0.86[ASN][1000 genomes]
rs4113659	0.86[ASN][1000 genomes]
rs4113661	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4113662	0.86[ASN][1000 genomes]
rs41308623	0.81[ASN][1000 genomes]
rs426563	1.00[JPT][hapmap]
rs4318454	0.84[ASN][1000 genomes]
rs4343537	0.86[ASN][1000 genomes]
rs4368405	0.84[ASN][1000 genomes]
rs447808	1.00[JPT][hapmap]
rs4574179	0.86[ASN][1000 genomes]
rs4813579	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815436	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4815438	0.86[LWK][hapmap];0.80[YRI][hapmap]
rs4815450	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57638633	0.86[ASN][1000 genomes]
rs59399848	0.84[ASN][1000 genomes]
rs6037128	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6037131	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6037133	1.00[JPT][hapmap]
rs6037159	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037161	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037164	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037166	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6037167	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6037168	0.81[ASN][1000 genomes]
rs6037169	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6037179	0.86[ASN][1000 genomes]
rs6037180	0.86[ASN][1000 genomes]
rs6037193	0.86[ASN][1000 genomes]
rs6037195	0.82[JPT][hapmap]
rs6037196	1.00[JPT][hapmap]
rs6037198	0.86[ASN][1000 genomes]
rs6037199	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6037204	0.81[ASN][1000 genomes]
rs6037206	0.84[ASN][1000 genomes]
rs6037208	0.86[ASN][1000 genomes]
rs6037212	0.86[ASN][1000 genomes]
rs6037217	0.86[ASN][1000 genomes]
rs6037220	0.86[ASN][1000 genomes]
rs6037222	0.82[JPT][hapmap]
rs6037223	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs60463280	0.84[ASN][1000 genomes]
rs6050663	1.00[JPT][hapmap]
rs6050707	0.81[ASN][1000 genomes]
rs6050709	0.81[ASN][1000 genomes]
rs6050710	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050712	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050714	0.81[ASN][1000 genomes]
rs6050717	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050720	0.81[ASN][1000 genomes]
rs6050723	0.81[ASN][1000 genomes]
rs6050724	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050725	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050726	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050727	0.81[ASN][1000 genomes]
rs6050729	0.81[ASN][1000 genomes]
rs6050730	0.81[ASN][1000 genomes]
rs6050732	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050733	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6050737	0.81[ASN][1000 genomes]
rs6050743	0.81[ASN][1000 genomes]
rs6050745	0.86[ASN][1000 genomes]
rs6050749	0.86[ASN][1000 genomes]
rs6050753	0.86[ASN][1000 genomes]
rs6050754	0.86[ASN][1000 genomes]
rs6050755	0.86[ASN][1000 genomes]
rs6050756	0.86[ASN][1000 genomes]
rs6050757	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050758	0.86[ASN][1000 genomes]
rs6050760	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050763	0.81[ASN][1000 genomes]
rs6050765	0.86[ASN][1000 genomes]
rs6050767	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6050768	0.86[ASN][1000 genomes]
rs6050770	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6050775	0.86[ASN][1000 genomes]
rs6050779	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6050787	0.86[ASN][1000 genomes]
rs6050788	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050789	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050791	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6050795	0.86[ASN][1000 genomes]
rs6050796	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050799	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6050801	0.84[ASN][1000 genomes]
rs6050802	0.86[ASN][1000 genomes]
rs6050804	0.86[ASN][1000 genomes]
rs6050805	0.84[ASN][1000 genomes]
rs6050807	0.84[ASN][1000 genomes]
rs6050809	0.86[ASN][1000 genomes]
rs6050814	0.82[AFR][1000 genomes]
rs6050832	0.86[ASN][1000 genomes]
rs6050833	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050834	0.86[ASN][1000 genomes]
rs6050835	0.86[ASN][1000 genomes]
rs6050838	0.86[ASN][1000 genomes]
rs6050840	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050841	0.86[ASN][1000 genomes]
rs6050846	0.86[ASN][1000 genomes]
rs6050847	0.86[ASN][1000 genomes]
rs6050848	0.86[ASN][1000 genomes]
rs6050851	0.86[ASN][1000 genomes]
rs6050853	0.86[ASN][1000 genomes]
rs6050854	0.86[ASN][1000 genomes]
rs6050858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050867	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6083886	1.00[JPT][hapmap]
rs6083896	1.00[JPT][hapmap]
rs6083897	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs6083899	1.00[JPT][hapmap]
rs61052177	0.84[ASN][1000 genomes]
rs6115200	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6115214	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6115215	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6115224	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6115232	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132848	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6132850	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6138588	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6138600	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6138612	1.00[JPT][hapmap]
rs7266130	1.00[JPT][hapmap]
rs7266592	1.00[JPT][hapmap]
rs73341361	0.86[ASN][1000 genomes]
rs73341363	0.84[ASN][1000 genomes]
rs73341365	0.84[ASN][1000 genomes]
rs73341397	0.86[ASN][1000 genomes]
rs73343217	0.86[ASN][1000 genomes]
rs73343255	0.86[ASN][1000 genomes]
rs73343275	0.84[ASN][1000 genomes]
rs73343292	0.84[ASN][1000 genomes]
rs73345232	0.86[ASN][1000 genomes]
rs7346687	0.86[ASN][1000 genomes]
rs742435	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs8115742	1.00[JPT][hapmap]
rs8116267	1.00[JPT][hapmap]
rs8117181	1.00[JPT][hapmap]
rs8120065	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8120594	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8121013	0.81[ASN][1000 genomes]
rs8121648	1.00[JPT][hapmap]
rs8126236	0.81[ASN][1000 genomes]
rs926486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs926487	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs928121	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9753575	0.86[ASN][1000 genomes]
rs981440	0.86[ASN][1000 genomes]
rs981441	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][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	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1056288	chr20:25662941-25744711	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1057618	chr20:25665455-25744711	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4815445	NANP	cis	cerebellum	SCAN
rs4815445	NINL	cis	Nerve Tibial	GTEx
rs4815445	VSX1	cis	cerebellum	SCAN
rs4815445	CST2	cis	parietal	SCAN
rs4815445	ZNF337	cis	Thyroid	GTEx
rs4815445	ZNF337	cis	lymphoblastoid	seeQTL
rs4815445	ZNF337	cis	cerebellum	SCAN
rs4815445	RP4-694B14.5	cis	Thyroid	GTEx
rs4815445	ENTPD6	cis	parietal	SCAN
rs4815445	ZNF337	cis	Stomach	GTEx
rs4815445	RP4-694B14.5	cis	lung	GTEx
rs4815445	ZNF337	cis	lung	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25657400-25676200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr20:25657600-25676000	Weak transcription	Stomach Mucosa	stomach
3	chr20:25657600-25676200	Weak transcription	Hela-S3	cervix
4	chr20:25657600-25676200	Weak transcription	K562	blood
5	chr20:25657600-25676400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr20:25657800-25676000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr20:25657800-25676200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr20:25657800-25676200	Weak transcription	Colonic Mucosa	Colon
9	chr20:25657800-25676200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:25658200-25676200	Weak transcription	Fetal Kidney	kidney
11	chr20:25658400-25676200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:25658800-25676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr20:25659000-25676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr20:25660600-25676000	Weak transcription	HUVEC	blood vessel
15	chr20:25662400-25676000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr20:25663800-25676000	Weak transcription	HMEC	breast
17	chr20:25664000-25676000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr20:25664000-25676000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr20:25664200-25676000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr20:25666400-25676000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr20:25666400-25676400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr20:25666800-25676000	Weak transcription	Brain Substantia Nigra	brain
23	chr20:25666800-25676200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:25666800-25676400	Weak transcription	Ovary	ovary
25	chr20:25667000-25676000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr20:25667000-25676000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr20:25667000-25676000	Weak transcription	Spleen	Spleen
28	chr20:25667000-25676000	Weak transcription	NHEK	skin
29	chr20:25667000-25676200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr20:25667000-25676200	Weak transcription	Liver	Liver
31	chr20:25667000-25676200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr20:25667200-25676000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr20:25667200-25676000	Weak transcription	Colon Smooth Muscle	Colon
34	chr20:25667200-25676000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr20:25667200-25676000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr20:25667200-25676200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr20:25667200-25676200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:25667200-25676200	Weak transcription	Right Ventricle	heart
39	chr20:25667400-25676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr20:25667400-25676000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr20:25667400-25676000	Weak transcription	Brain Anterior Caudate	brain
42	chr20:25667400-25676000	Weak transcription	Psoas Muscle	Psoas
43	chr20:25667400-25676000	Weak transcription	NHDF-Ad	bronchial
44	chr20:25667400-25676200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr20:25667400-25676200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr20:25667400-25676200	Weak transcription	Fetal Intestine Large	intestine
47	chr20:25667400-25676200	Weak transcription	Fetal Intestine Small	intestine
48	chr20:25667400-25676200	Weak transcription	Pancreas	Pancrea
49	chr20:25667400-25676400	Weak transcription	Aorta	Aorta
50	chr20:25667400-25676600	Weak transcription	Gastric	stomach

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