Variant report

Variant	rs6852979
Chromosome Location	chr4:151260886-151260887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11929842	0.84[ASN][1000 genomes]
rs11933443	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11944163	0.87[ASN][1000 genomes]
rs12505042	0.84[ASN][1000 genomes]
rs12643608	0.87[ASN][1000 genomes]
rs12644110	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12711271	0.84[EUR][1000 genomes]
rs13116727	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121248	0.89[ASN][1000 genomes]
rs1472842	0.89[ASN][1000 genomes]
rs1599167	0.84[ASN][1000 genomes]
rs17504145	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1813134	0.83[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1870515	0.81[ASN][1000 genomes]
rs1960918	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290847	0.84[ASN][1000 genomes]
rs2292206	0.83[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2292207	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35016840	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35370115	0.89[ASN][1000 genomes]
rs35766906	0.89[ASN][1000 genomes]
rs62344533	0.89[ASN][1000 genomes]
rs6535728	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6837957	0.83[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6850249	0.84[ASN][1000 genomes]
rs7653994	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654538	0.84[ASN][1000 genomes]
rs7655683	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7657477	0.84[ASN][1000 genomes]
rs7677474	0.83[ASN][1000 genomes]
rs7677475	0.83[ASN][1000 genomes]
rs7685302	0.84[ASN][1000 genomes]
rs962626	0.83[CEU][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	nsv880259	chr4:151210761-151367745	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv880260	chr4:151214038-151331191	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	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
8	nsv830112	chr4:151243801-151431771	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6852979	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs6852979	PLRG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151205000-151272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr4:151224200-151274800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:151226800-151272400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr4:151227400-151269400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:151233400-151264200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:151233400-151264200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:151236400-151272600	Weak transcription	Thymus	Thymus
8	chr4:151236800-151264200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:151238200-151270200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:151242600-151268600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:151242800-151273800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:151243000-151277000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:151243000-151277400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:151243000-151312000	Weak transcription	Primary B cells from cord blood	blood
15	chr4:151244200-151300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:151245000-151270400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:151245400-151264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:151245400-151268200	Weak transcription	Esophagus	oesophagus
19	chr4:151245800-151268000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:151247200-151277000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr4:151247400-151264200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:151247600-151269800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:151247800-151261600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:151247800-151261800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:151247800-151285200	Weak transcription	GM12878-XiMat	blood
26	chr4:151248000-151261800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:151248000-151268000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr4:151248200-151269800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:151248800-151261200	Weak transcription	Primary T cells from cord blood	blood
30	chr4:151249000-151261000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:151253600-151264200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:151259200-151269400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:151259400-151264200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:151259400-151264400	Weak transcription	K562	blood
35	chr4:151259400-151277000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:151259600-151263800	Weak transcription	Liver	Liver
37	chr4:151259800-151263200	Weak transcription	Ovary	ovary
38	chr4:151259800-151264000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:151259800-151264000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:151259800-151264600	Weak transcription	Right Ventricle	heart
41	chr4:151259800-151267000	Weak transcription	Left Ventricle	heart
42	chr4:151259800-151267000	Weak transcription	Pancreas	Pancrea
43	chr4:151259800-151268200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:151259800-151269000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:151259800-151269000	Weak transcription	Osteobl	bone
46	chr4:151260000-151263600	Weak transcription	Fetal Heart	heart
47	chr4:151260000-151263800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr4:151260000-151264000	Weak transcription	Fetal Lung	lung
49	chr4:151260000-151266800	Weak transcription	Fetal Intestine Small	intestine
50	chr4:151260000-151280000	Weak transcription	Fetal Stomach	stomach

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