Variant report

Variant	rs1976494
Chromosome Location	chr4:151481857-151481858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10006803	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10012087	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10015104	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10018886	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10022844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10030673	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12649589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13104084	0.91[ASN][1000 genomes]
rs13124512	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13127921	0.92[ASN][1000 genomes]
rs13134428	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13145262	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150736	0.92[ASN][1000 genomes]
rs13151692	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1394496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1504785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1566867	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857750	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4380502	0.88[ASN][1000 genomes]
rs4413387	0.88[ASN][1000 genomes]
rs7686589	0.83[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap]
rs7690080	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs991529	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9993229	0.92[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs9994153	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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	esv3377418	chr4:151479802-151482200	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1976494	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs1976494	TMEM184C	cis	cerebellum	SCAN
rs1976494	ARHGAP10	cis	parietal	SCAN

Chromatin state (count:29 , 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	chr4:151472000-151483000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:151472000-151490000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr4:151472000-151501400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:151472600-151500200	Weak transcription	Aorta	Aorta
6	chr4:151473200-151484000	Weak transcription	Fetal Kidney	kidney
7	chr4:151473400-151486000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:151473400-151491200	Weak transcription	Ovary	ovary
9	chr4:151474200-151489600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:151474800-151486400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:151475200-151486200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:151475400-151486000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:151475400-151486200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:151475400-151486200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:151475400-151486400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:151475600-151486000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr4:151475600-151486000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:151475600-151486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:151477200-151486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:151477200-151486400	Weak transcription	Fetal Intestine Small	intestine
21	chr4:151477200-151502400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:151478400-151486200	Weak transcription	Primary B cells from cord blood	blood
23	chr4:151478800-151489600	Weak transcription	A549	lung
24	chr4:151479200-151486200	Weak transcription	Primary T cells from cord blood	blood
25	chr4:151479400-151490200	Weak transcription	K562	blood
26	chr4:151479400-151500800	Weak transcription	Lung	lung
27	chr4:151479600-151501800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr4:151480600-151500800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:151481200-151500400	Weak transcription	Rectal Mucosa Donor 31	rectum

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