Variant report

Variant	rs751857
Chromosome Location	chr19:19602873-19602874
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19602336..19605055-chr19:19620570..19622403,2	MCF-7	breast:
2	chr19:19430093..19431737-chr19:19601743..19604331,2	MCF-7	breast:
3	chr19:19514390..19517694-chr19:19598526..19603373,7	K562	blood:
4	chr19:19514543..19521149-chr19:19597604..19603543,11	MCF-7	breast:
5	chr19:19518514..19520258-chr19:19600327..19603326,2	K562	blood:
6	chr19:19591413..19595730-chr19:19599673..19603116,5	K562	blood:
7	chr19:19602828..19604988-chr19:19663749..19665347,2	MCF-7	breast:
8	chr19:19601950..19605633-chr19:19625984..19629192,3	K562	blood:
9	chr19:19513509..19518475-chr19:19595979..19603373,11	K562	blood:
10	chr19:19600750..19602890-chr19:19604803..19607283,5	K562	blood:
11	chr19:19493350..19496706-chr19:19599997..19602939,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000129933	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000178093	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1036215	0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs10406278	0.85[EUR][1000 genomes]
rs11085264	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11668203	0.92[EUR][1000 genomes]
rs11669558	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11669730	1.00[ASW][hapmap];0.92[GIH][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670687	0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670761	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670775	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670882	0.84[TSI][hapmap];0.94[EUR][1000 genomes]
rs11671253	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1529745	0.83[EUR][1000 genomes]
rs1560687	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16996127	0.83[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.98[EUR][1000 genomes]
rs17684164	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17751061	0.87[TSI][hapmap]
rs2011503	0.81[ASW][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap]
rs2060274	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2060275	0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2905429	0.80[AMR][1000 genomes]
rs2905434	0.84[EUR][1000 genomes]
rs2916070	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2916072	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2916075	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2965179	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965181	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2965184	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2965186	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs2965190	0.92[GIH][hapmap];0.81[TSI][hapmap]
rs2965195	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs2965201	0.81[ASW][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap]
rs34487417	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34667451	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45556231	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45631651	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808204	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4808205	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808206	0.91[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808951	0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808958	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4808962	0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4808968	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808969	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808970	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55927782	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56280531	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56291054	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56330647	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58074958	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61744761	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7245689	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7250233	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7252453	0.95[EUR][1000 genomes]
rs7256028	0.98[EUR][1000 genomes]
rs754256	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs756997	0.90[YRI][hapmap]
rs8100927	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8101219	0.91[ASW][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8102502	0.84[TSI][hapmap];0.93[EUR][1000 genomes]
rs8105642	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8110171	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8110250	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8111093	0.83[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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs751857	IL12RB1	cis	parietal	SCAN
rs751857	LSM4	cis	cerebellum	SCAN
rs751857	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs751857	YJEFN3	cis	cerebellum	SCAN
rs751857	GATAD2A	cis	parietal	SCAN
rs751857	DDX49	cis	cerebellum	SCAN
rs751857	LRRC25	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19599000-19618000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:19600800-19619400	Strong transcription	Dnd41	blood
3	chr19:19601000-19603800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:19601000-19606800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:19601000-19624600	Weak transcription	Fetal Brain Male	brain
6	chr19:19601200-19603000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:19601200-19603000	Weak transcription	Right Ventricle	heart
8	chr19:19601200-19603200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:19601200-19603200	Weak transcription	Lung	lung
10	chr19:19601200-19603400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:19601200-19603400	Weak transcription	Ovary	ovary
12	chr19:19601200-19603400	Weak transcription	HMEC	breast
13	chr19:19601200-19604000	Weak transcription	Small Intestine	intestine
14	chr19:19601200-19604800	Weak transcription	HSMMtube	muscle
15	chr19:19601200-19605200	Weak transcription	Aorta	Aorta
16	chr19:19601200-19624800	Weak transcription	Fetal Kidney	kidney
17	chr19:19601200-19624800	Weak transcription	Right Atrium	heart
18	chr19:19601400-19603000	Weak transcription	Brain Angular Gyrus	brain
19	chr19:19601400-19603000	Weak transcription	Brain Germinal Matrix	brain
20	chr19:19601400-19603000	Weak transcription	Fetal Lung	lung
21	chr19:19601400-19603000	Weak transcription	GM12878-XiMat	blood
22	chr19:19601400-19603200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:19601400-19603200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:19601400-19603200	Weak transcription	Left Ventricle	heart
25	chr19:19601400-19603200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:19601400-19603400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:19601400-19603400	Weak transcription	HSMM	muscle
28	chr19:19601400-19604000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:19601400-19604000	Weak transcription	HUVEC	blood vessel
30	chr19:19601400-19604200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:19601400-19604200	Weak transcription	NH-A	brain
32	chr19:19601400-19604200	Weak transcription	NHDF-Ad	bronchial
33	chr19:19601400-19604800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:19601400-19604800	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:19601400-19604800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:19601400-19604800	Weak transcription	Hela-S3	cervix
37	chr19:19601400-19605000	Weak transcription	Brain Anterior Caudate	brain
38	chr19:19601400-19605200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:19601400-19605200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:19601400-19605200	Weak transcription	Brain Substantia Nigra	brain
41	chr19:19601400-19605200	Weak transcription	Stomach Mucosa	stomach
42	chr19:19601400-19609200	Weak transcription	Psoas Muscle	Psoas
43	chr19:19601400-19611800	Strong transcription	K562	blood
44	chr19:19601400-19612200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:19601400-19615200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:19601400-19619400	Strong transcription	Fetal Intestine Small	intestine
47	chr19:19601400-19624800	Weak transcription	Fetal Heart	heart
48	chr19:19601600-19603400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:19601600-19603600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:19601600-19603800	Weak transcription	Primary B cells from cord blood	blood

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