Variant report

Variant	rs8102502
Chromosome Location	chr19:19652746-19652747
allele	C/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	chr19:19651192..19652936-chr19:19774066..19776214,2	MCF-7	breast:
2	chr19:19431326..19434090-chr19:19651434..19653911,2	K562	blood:
3	chr19:19650831..19653075-chr19:20010995..20012617,3	K562	blood:
4	chr19:19626939..19628497-chr19:19651278..19652936,2	K562	blood:
5	chr19:19625365..19628497-chr19:19651436..19653967,3	K562	blood:
6	chr19:19650697..19653588-chr19:19753029..19754860,3	K562	blood:
7	chr19:19652335..19654286-chr19:19738198..19739867,2	MCF-7	breast:
8	chr19:19649879..19653588-chr19:19753029..19755939,4	K562	blood:
9	chr19:19652327..19654273-chr19:19657825..19660642,2	MCF-7	breast:
10	chr19:19651405..19654732-chr19:19727842..19732175,4	MCF-7	breast:
11	chr19:19649600..19655493-chr19:19770960..19774805,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184635	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000105717	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000267268	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000129933	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10221485	0.94[ASN][1000 genomes]
rs1036215	0.94[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs11085264	0.94[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs11668203	0.86[EUR][1000 genomes]
rs11669558	0.91[EUR][1000 genomes]
rs11669730	0.82[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs11670687	0.93[EUR][1000 genomes]
rs11670761	0.94[EUR][1000 genomes]
rs11670775	0.94[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs11670882	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671253	0.93[EUR][1000 genomes]
rs1560687	0.94[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs16996127	0.94[CEU][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes]
rs17684164	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs1865036	0.94[ASN][1000 genomes]
rs2060274	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2060275	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2304097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2916070	0.94[CEU][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs2916072	0.86[EUR][1000 genomes]
rs2916075	0.86[EUR][1000 genomes]
rs2965179	0.82[EUR][1000 genomes]
rs2965181	0.82[EUR][1000 genomes]
rs2965184	0.94[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs2965186	0.93[CEU][hapmap];0.96[TSI][hapmap]
rs2965195	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs2965201	0.94[CEU][hapmap];0.96[TSI][hapmap]
rs34487417	0.80[EUR][1000 genomes]
rs34667451	0.93[EUR][1000 genomes]
rs45556231	0.94[EUR][1000 genomes]
rs45631651	0.94[EUR][1000 genomes]
rs4808204	0.93[EUR][1000 genomes]
rs4808205	0.94[EUR][1000 genomes]
rs4808206	0.94[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs4808951	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4808962	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs4808968	0.94[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs4808969	0.94[EUR][1000 genomes]
rs4808970	0.93[EUR][1000 genomes]
rs55927782	0.94[EUR][1000 genomes]
rs56280531	0.93[EUR][1000 genomes]
rs56291054	0.80[EUR][1000 genomes]
rs56330647	0.95[EUR][1000 genomes]
rs57368710	0.94[ASN][1000 genomes]
rs58074958	0.86[EUR][1000 genomes]
rs61744761	0.91[EUR][1000 genomes]
rs7245689	0.95[EUR][1000 genomes]
rs7249319	0.94[ASN][1000 genomes]
rs7250233	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs7252453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256028	0.95[EUR][1000 genomes]
rs751857	0.84[TSI][hapmap];0.93[EUR][1000 genomes]
rs754256	0.94[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs756997	0.94[CEU][hapmap]
rs8100927	0.94[EUR][1000 genomes]
rs8101219	0.94[EUR][1000 genomes]
rs8105642	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs8110171	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs8110250	0.94[CEU][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv543928	chr19:19649839-19664043	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8102502	GATAD2A	cis	parietal	SCAN
rs8102502	OCEL1	cis	parietal	SCAN
rs8102502	IL12RB1	cis	parietal	SCAN
rs8102502	JUND	cis	parietal	SCAN
rs8102502	DDX49	cis	cerebellum	SCAN
rs8102502	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs8102502	LSM4	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19650400-19653000	Bivalent Enhancer	Placenta	Placenta
3	chr19:19650800-19652800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:19650800-19652800	Enhancers	Fetal Heart	heart
5	chr19:19651400-19652800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:19651400-19652800	Bivalent Enhancer	Fetal Thymus	thymus
7	chr19:19651400-19653400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:19651600-19653000	Bivalent Enhancer	Fetal Stomach	stomach
9	chr19:19651600-19653200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr19:19651600-19653400	Enhancers	Spleen	Spleen
11	chr19:19651800-19653000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr19:19651800-19653400	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr19:19652000-19688400	Weak transcription	Right Atrium	heart
14	chr19:19652200-19652800	Bivalent Enhancer	Brain Germinal Matrix	brain
15	chr19:19652200-19652800	Bivalent Enhancer	Colonic Mucosa	Colon
16	chr19:19652200-19652800	Enhancers	HMEC	breast
17	chr19:19652200-19653000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr19:19652200-19653000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
19	chr19:19652200-19653200	Enhancers	Primary T cells from cord blood	blood
20	chr19:19652200-19653200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:19652200-19653400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr19:19652200-19653600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr19:19652200-19654000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:19652200-19654400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr19:19652200-19657600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:19652200-19658000	Weak transcription	Right Ventricle	heart
27	chr19:19652200-19680000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:19652400-19652800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:19652400-19652800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
30	chr19:19652400-19653000	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr19:19652400-19653000	Enhancers	Primary hematopoietic stem cells	blood
32	chr19:19652400-19653000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:19652400-19653000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:19652400-19653000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:19652400-19653200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr19:19652400-19653400	Enhancers	Primary B cells from cord blood	blood
37	chr19:19652400-19653400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr19:19652400-19653600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr19:19652400-19653600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:19652400-19653800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:19652400-19654200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr19:19652400-19655000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:19652400-19655600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:19652600-19652800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:19652600-19652800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:19652600-19652800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:19652600-19653200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr19:19652600-19653200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr19:19652600-19653400	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr19:19652600-19653600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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