Variant report

Variant	rs6508822
Chromosome Location	chr19:39355676-39355677
allele	A/G
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	chr19:39350563..39353350-chr19:39354978..39358283,3	MCF-7	breast:
2	chr19:39326842..39329688-chr19:39354177..39355882,2	K562	blood:
3	chr19:39355316..39357305-chr19:39358972..39361148,3	MCF-7	breast:
4	chr19:39328808..39331038-chr19:39355498..39358210,2	MCF-7	breast:
5	chr19:39338783..39344716-chr19:39351762..39356757,15	MCF-7	breast:
6	chr19:39339063..39344846-chr19:39351660..39355862,7	MCF-7	breast:
7	chr19:39355225..39357682-chr19:39363417..39365979,2	MCF-7	breast:
8	chr19:39341098..39344560-chr19:39351786..39356667,5	K562	blood:
9	chr19:39354973..39357076-chr19:39358619..39360688,2	MCF-7	breast:
10	chr19:39328430..39329992-chr19:39354096..39356995,2	MCF-7	breast:
11	chr19:39327808..39329688-chr19:39353305..39355677,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction
ENSG00000187994	Chromatin interaction
ENSG00000269050	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1001413	0.89[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1103435	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2113123	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs2113124	0.89[EUR][1000 genomes]
rs2278009	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278011	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278012	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2318459	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28496951	0.91[CHB][hapmap]
rs67859595	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7246134	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7255774	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs8100220	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8104416	0.88[EUR][1000 genomes]
rs8104420	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs862455	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs862459	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs862464	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9789283	0.84[EUR][1000 genomes]

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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6508822	HNRNPL	Cis_1M	lymphoblastoid	RTeQTL
rs6508822	HNRNPL	cis	lymphoblastoid	seeQTL
rs6508822	HNRNPL	N/A	lymphoblastoid	RTeQTL
rs6508822	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39343600-39359800	Weak transcription	Small Intestine	intestine
2	chr19:39344200-39356400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:39348600-39359600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:39349400-39359800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39352400-39356600	Enhancers	Fetal Muscle Trunk	muscle
6	chr19:39352400-39357000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:39352800-39357200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:39353200-39358000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr19:39353400-39357800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr19:39353400-39359600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr19:39353400-39363800	Weak transcription	HSMMtube	muscle
12	chr19:39353600-39356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:39353600-39356600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:39353600-39356600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:39353600-39357000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr19:39353600-39359200	Weak transcription	Esophagus	oesophagus
17	chr19:39353600-39359600	Weak transcription	Liver	Liver
18	chr19:39353600-39359600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr19:39353600-39359800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr19:39353600-39359800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:39353600-39359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:39353600-39359800	Weak transcription	Colonic Mucosa	Colon
23	chr19:39353600-39359800	Weak transcription	Fetal Lung	lung
24	chr19:39353600-39359800	Weak transcription	Lung	lung
25	chr19:39353800-39357000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr19:39354000-39356800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:39354000-39356800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr19:39354000-39359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:39354000-39359200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:39354000-39359600	Weak transcription	Right Atrium	heart
31	chr19:39354000-39359800	Weak transcription	Psoas Muscle	Psoas
32	chr19:39354000-39359800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:39354200-39355800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr19:39354200-39356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:39354200-39357200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr19:39354200-39357600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr19:39354400-39359800	Weak transcription	Left Ventricle	heart
38	chr19:39354800-39356200	Enhancers	HUVEC	blood vessel
39	chr19:39354800-39356800	Enhancers	Adipose Nuclei	Adipose
40	chr19:39354800-39357000	Enhancers	Placenta	Placenta
41	chr19:39354800-39358000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr19:39355000-39355800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:39355000-39356000	Enhancers	Hela-S3	cervix
44	chr19:39355000-39356200	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr19:39355000-39356200	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr19:39355000-39356200	Flanking Active TSS	GM12878-XiMat	blood
47	chr19:39355000-39356800	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr19:39355000-39357000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:39355000-39358000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr19:39355000-39358200	Enhancers	Primary T cells from cord blood	blood

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