Variant report

Variant	rs4803573
Chromosome Location	chr19:38424558-38424559
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:
3	chr19:38424099..38425742-chr19:38427157..38428812,2	K562	blood:
4	chr19:38405526..38407086-chr19:38423053..38425586,2	MCF-7	breast:
5	chr19:38423561..38425591-chr19:38488215..38490133,2	MCF-7	breast:
6	chr19:38423922..38426366-chr19:38436893..38438716,2	MCF-7	breast:
7	chr19:38423743..38426556-chr19:38482738..38484356,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10404159	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10404567	0.88[CEU][hapmap];0.85[GIH][hapmap]
rs10415399	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420746	0.88[CEU][hapmap]
rs11083441	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1119229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs12608883	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1291	0.88[CEU][hapmap]
rs12973580	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12974225	0.88[CEU][hapmap]
rs1643460	0.83[EUR][1000 genomes]
rs1643461	0.87[EUR][1000 genomes]
rs1643466	0.87[CEU][hapmap]
rs1643467	0.87[CEU][hapmap]
rs1643468	0.87[CEU][hapmap]
rs1725481	0.88[CEU][hapmap]
rs1725482	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs1725499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075281	0.88[CEU][hapmap]
rs241932	0.88[CEU][hapmap]
rs28460297	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3095726	0.82[CEU][hapmap]
rs353410	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs353411	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353414	0.87[CEU][hapmap]
rs353415	0.88[CEU][hapmap]
rs353423	0.87[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3865514	1.00[YRI][hapmap]
rs4239516	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802144	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802147	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802151	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap]
rs4803551	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705492	0.88[CEU][hapmap]
rs705493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs705495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705499	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs8102579	0.88[CEU][hapmap]
rs8108434	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109053	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8109835	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110284	0.87[CEU][hapmap]
rs8112706	0.87[CEU][hapmap]
rs8113273	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs833895	0.87[CEU][hapmap]
rs833926	0.88[CEU][hapmap]
rs856300	0.82[CEU][hapmap]
rs856304	0.88[CEU][hapmap]

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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4803573	CBLC	cis	parietal	SCAN
rs4803573	PHLDB3	cis	parietal	SCAN
rs4803573	DMPK	cis	parietal	SCAN
rs4803573	PHLDB3	cis	cerebellum	SCAN
rs4803573	XRCC1	cis	parietal	SCAN
rs4803573	PAFAH1B3	cis	cerebellum	SCAN
rs4803573	LIPE	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:38411800-38426200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:38418800-38425600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:38419400-38424800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:38420200-38425000	Weak transcription	Small Intestine	intestine
8	chr19:38421200-38425000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:38421600-38424800	Enhancers	Fetal Thymus	thymus
10	chr19:38421800-38425400	Enhancers	Fetal Muscle Trunk	muscle
11	chr19:38421800-38425400	Enhancers	Fetal Muscle Leg	muscle
12	chr19:38422000-38426400	Weak transcription	Primary T cells from cord blood	blood
13	chr19:38422200-38425000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:38422200-38425600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:38422400-38424600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:38422400-38424800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:38422400-38424800	Enhancers	Left Ventricle	heart
18	chr19:38422400-38424800	Enhancers	HUVEC	blood vessel
19	chr19:38422400-38425000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:38422400-38425000	Enhancers	Psoas Muscle	Psoas
21	chr19:38422400-38425000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr19:38422600-38425000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:38423000-38425200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:38423000-38425400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:38423000-38438200	Weak transcription	Brain Angular Gyrus	brain
26	chr19:38423200-38425000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:38423200-38425000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr19:38423200-38425000	Enhancers	HSMMtube	muscle
29	chr19:38423200-38425800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr19:38423200-38426000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:38423200-38426200	Weak transcription	Ovary	ovary
32	chr19:38423200-38426600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr19:38423400-38424600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:38423400-38425000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr19:38423400-38425000	Enhancers	Esophagus	oesophagus
37	chr19:38423400-38425200	Enhancers	HSMM	muscle
38	chr19:38423400-38425200	Enhancers	NH-A	brain
39	chr19:38423400-38425800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr19:38423400-38426000	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:38423400-38426000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr19:38423400-38426400	Weak transcription	Brain Germinal Matrix	brain
43	chr19:38423400-38427600	Enhancers	Liver	Liver
44	chr19:38423400-38433800	Weak transcription	Thymus	Thymus
45	chr19:38423600-38424600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:38423600-38424600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr19:38423600-38424600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr19:38423600-38424600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr19:38423600-38424600	Enhancers	Primary hematopoietic stem cells	blood
50	chr19:38423600-38424600	Enhancers	Duodenum Smooth Muscle	Duodenum

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