Variant report

Variant	rs17589398
Chromosome Location	chr4:151496759-151496760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:151495871..151498604-chr4:151499774..151501672,2	K562	blood:
2	chr4:151494137..151496884-chr4:151503865..151506422,4	K562	blood:
3	chr4:151236254..151238436-chr4:151495963..151498535,2	K562	blood:
4	chr4:151487662..151490527-chr4:151494648..151496977,2	K562	blood:
5	chr4:151495333..151496884-chr4:151503356..151505383,3	K562	blood:
6	chr4:151491888..151494429-chr4:151494545..151497741,3	K562	blood:

Variant related genes	Relation type
ENSG00000198589	Chromatin interaction
ENSG00000249690	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11722416	0.82[ASN][1000 genomes]
rs11727995	0.81[ASN][1000 genomes]
rs11729560	0.87[ASN][1000 genomes]
rs11932482	0.87[ASN][1000 genomes]
rs11936646	0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs11937036	0.84[ASN][1000 genomes]
rs11940101	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs11944485	0.91[AFR][1000 genomes]
rs17504868	0.87[ASN][1000 genomes]
rs17504952	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs17589182	0.85[ASN][1000 genomes]
rs36187100	0.82[ASN][1000 genomes]
rs4370117	1.00[ASW][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs4413388	0.82[ASN][1000 genomes]
rs4593110	0.82[ASN][1000 genomes]
rs4696185	0.87[ASN][1000 genomes]
rs4696458	0.82[ASN][1000 genomes]
rs55977492	0.85[ASN][1000 genomes]
rs55998463	0.82[ASN][1000 genomes]
rs56671775	0.87[ASN][1000 genomes]
rs57452017	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58633621	0.87[ASN][1000 genomes]
rs62344697	0.80[ASN][1000 genomes]
rs62344699	0.82[ASN][1000 genomes]
rs62344702	0.85[ASN][1000 genomes]
rs62344705	0.87[ASN][1000 genomes]
rs62344742	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72734489	0.82[ASN][1000 genomes]
rs72734495	0.87[ASN][1000 genomes]
rs7690365	0.82[ASN][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	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869051	chr4:151347901-151737781	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1018942	chr4:151423295-151556444	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv537301	chr4:151423295-151556444	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv4547	chr4:151486280-151531479	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription 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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17589398	LRBA	cis	parietal	SCAN
rs17589398	CHRM3	trans	parietal	SCAN
rs17589398	LRBA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151470400-151503600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr4:151472000-151501400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:151472600-151500200	Weak transcription	Aorta	Aorta
4	chr4:151477200-151502400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:151479400-151500800	Weak transcription	Lung	lung
6	chr4:151479600-151501800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:151480600-151500800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:151481200-151500400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:151486600-151499800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:151486600-151500000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:151486600-151500000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:151486600-151500200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:151486600-151500800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:151486600-151503200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:151486600-151510400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:151487000-151502400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr4:151487000-151503200	Weak transcription	Primary B cells from cord blood	blood
18	chr4:151487200-151655000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:151490800-151499000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:151490800-151503800	Weak transcription	HMEC	breast
21	chr4:151491200-151499000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:151491600-151499800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:151491600-151500000	Weak transcription	HSMM	muscle
24	chr4:151491600-151501400	Weak transcription	Primary T cells from cord blood	blood
25	chr4:151492200-151500400	Weak transcription	Esophagus	oesophagus
26	chr4:151494000-151500800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:151494400-151498000	Active TSS	Colon Smooth Muscle	Colon
28	chr4:151494400-151499000	Weak transcription	Fetal Intestine Large	intestine
29	chr4:151494400-151499800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:151494400-151500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:151494400-151500800	Weak transcription	Gastric	stomach
32	chr4:151494400-151500800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:151494600-151500000	Weak transcription	Pancreas	Pancrea
34	chr4:151494600-151500800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:151494600-151500800	Weak transcription	Left Ventricle	heart
36	chr4:151495000-151499400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:151495000-151499800	Weak transcription	Osteobl	bone
38	chr4:151495000-151500000	Weak transcription	NH-A	brain
39	chr4:151495200-151499800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:151495200-151500200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:151495200-151500400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:151495200-151504000	Weak transcription	NHEK	skin
43	chr4:151495400-151500000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:151495600-151499800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:151495600-151500600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:151495600-151500800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:151496000-151499000	Enhancers	Rectal Smooth Muscle	rectum
48	chr4:151496200-151499000	Weak transcription	A549	lung
49	chr4:151496200-151500000	Weak transcription	K562	blood
50	chr4:151496600-151496800	Active TSS	Duodenum Smooth Muscle	Duodenum

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