Variant report

Variant	rs1979920
Chromosome Location	chr4:151343482-151343483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12498862	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12499470	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12500337	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12502486	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12503093	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506612	0.93[ASN][1000 genomes]
rs12507785	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12508149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647325	0.84[ASN][1000 genomes]
rs17504359	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17504442	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17589028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589134	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589349	0.84[ASN][1000 genomes]
rs2036552	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2360071	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41386148	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56714695	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6535735	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6812262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817796	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827645	0.84[ASN][1000 genomes]
rs6831707	0.84[ASN][1000 genomes]
rs6833359	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6836012	0.84[ASN][1000 genomes]
rs6839345	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6849869	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6854612	0.85[ASN][1000 genomes]
rs7677055	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7681051	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7699001	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8180280	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs952097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs998069	0.84[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	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	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
3	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
4	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
5	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
6	esv3375859	chr4:151340527-151343875	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3324942	chr4:151340802-151343550	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1979920	PLRG1	cis	parietal	SCAN
rs1979920	LRBA	cis	cerebellum	SCAN
rs1979920	TTC29	cis	cerebellum	SCAN
rs1979920	FAM160A1	cis	parietal	SCAN
rs1979920	LRBA	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151272000-151371400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:151286600-151355600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:151290200-151367400	Weak transcription	K562	blood
4	chr4:151292400-151361000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:151307000-151348800	Weak transcription	Aorta	Aorta
6	chr4:151311600-151343800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:151313200-151358200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:151313600-151358000	Weak transcription	GM12878-XiMat	blood
9	chr4:151315600-151344000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:151315800-151359400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr4:151317400-151358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:151319000-151371000	Weak transcription	Left Ventricle	heart
13	chr4:151324400-151343600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:151324400-151344000	Weak transcription	Gastric	stomach
15	chr4:151324600-151344000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:151328800-151344200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:151331400-151358800	Weak transcription	Liver	Liver
18	chr4:151332800-151353000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:151333000-151343800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:151333000-151357800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:151333000-151408000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:151333200-151351600	Weak transcription	Primary B cells from cord blood	blood
23	chr4:151333600-151355600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr4:151334200-151347200	Weak transcription	Fetal Thymus	thymus
25	chr4:151334600-151345800	Weak transcription	NHEK	skin
26	chr4:151334800-151344400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:151335400-151352800	Weak transcription	Esophagus	oesophagus
28	chr4:151336800-151343600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:151337200-151363200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:151340600-151346000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:151341200-151343600	Weak transcription	Thymus	Thymus
32	chr4:151341400-151343600	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:151342200-151343800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:151342200-151344000	Weak transcription	Pancreas	Pancrea
35	chr4:151342200-151344000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:151342200-151344000	Weak transcription	Spleen	Spleen
37	chr4:151342600-151344000	Weak transcription	Adipose Nuclei	Adipose
38	chr4:151342800-151343600	Strong transcription	Primary T cells from cord blood	blood
39	chr4:151342800-151345000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:151342800-151345000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:151342800-151345200	Weak transcription	Brain Germinal Matrix	brain
42	chr4:151342800-151345200	Strong transcription	Fetal Intestine Small	intestine
43	chr4:151342800-151346000	Strong transcription	Fetal Intestine Large	intestine
44	chr4:151343000-151343800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr4:151343000-151344000	Weak transcription	Small Intestine	intestine
46	chr4:151343000-151344600	Strong transcription	Fetal Stomach	stomach
47	chr4:151343000-151344800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:151343000-151345000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:151343000-151345400	Weak transcription	Colonic Mucosa	Colon
50	chr4:151343000-151345400	Weak transcription	Right Ventricle	heart

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