Variant report

Variant	rs999784
Chromosome Location	chr4:151208778-151208779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151207253..151208825-chr4:151218908..151221220,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10520053	0.81[EUR][1000 genomes]
rs11059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13134607	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17503902	0.80[EUR][1000 genomes]
rs1813250	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2085723	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085724	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3749574	0.81[EUR][1000 genomes]
rs6535727	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6817154	0.81[EUR][1000 genomes]
rs7656639	0.81[EUR][1000 genomes]
rs7657086	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7661359	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7691260	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv880257	chr4:151170387-151231371	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs999784	DCLK2	cis	cerebellum	SCAN
rs999784	ATP2B1	trans	parietal	SCAN
rs999784	LRBA	cis	normal skin	skin_eQTL
rs999784	LRBA	cis	lesional skin	skin_eQTL
rs999784	LRBA	cis	uninvolved skin	skin_eQTL
rs999784	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151181800-151209000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr4:151184800-151209200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
4	chr4:151192400-151232800	Weak transcription	Brain Substantia Nigra	brain
5	chr4:151193600-151210200	Weak transcription	HepG2	liver
6	chr4:151197200-151209400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:151198400-151209000	Strong transcription	Primary T cells from cord blood	blood
8	chr4:151202200-151208800	Weak transcription	Ovary	ovary
9	chr4:151202200-151210000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:151202200-151213200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:151202200-151218000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:151202400-151210400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:151202600-151210600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:151202600-151213200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:151202800-151210000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:151202800-151223800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:151203600-151218400	Weak transcription	Fetal Stomach	stomach
18	chr4:151203800-151211000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:151203800-151244400	Weak transcription	Fetal Thymus	thymus
20	chr4:151204000-151208800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:151204000-151211000	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:151204000-151223800	Weak transcription	K562	blood
23	chr4:151204000-151244600	Weak transcription	Lung	lung
24	chr4:151204200-151210600	Weak transcription	Liver	Liver
25	chr4:151204200-151213200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:151204600-151209400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:151204600-151210400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:151204600-151210400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:151204600-151213200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:151204600-151213600	Weak transcription	Aorta	Aorta
31	chr4:151204600-151216800	Weak transcription	Pancreas	Pancrea
32	chr4:151204600-151236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:151204600-151242200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr4:151204800-151209800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:151204800-151211000	Weak transcription	Fetal Intestine Small	intestine
36	chr4:151205000-151213200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:151205000-151236400	Weak transcription	Primary B cells from cord blood	blood
38	chr4:151205000-151272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:151205400-151212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:151205800-151210600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:151206400-151213200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:151206600-151222800	Weak transcription	Osteobl	bone
43	chr4:151206800-151223800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:151206800-151223800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:151207200-151208800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:151207200-151208800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr4:151207200-151209400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr4:151207200-151209400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:151207200-151210400	Weak transcription	GM12878-XiMat	blood
50	chr4:151207200-151226600	Weak transcription	Primary hematopoietic stem cells	blood

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