Variant report

Variant	rs2290846
Chromosome Location	chr4:151199080-151199081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10520053	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1080195	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722135	0.82[CHB][hapmap]
rs11728745	0.83[CHB][hapmap]
rs1507190	0.83[CHB][hapmap]
rs1507191	0.83[CHB][hapmap]
rs17503902	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17503964	0.83[CHB][hapmap]
rs17588356	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1824406	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056457	0.83[CHB][hapmap]
rs2085722	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749574	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696646	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696651	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696659	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696660	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55728314	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56169929	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59435073	0.83[ASN][1000 genomes]
rs62344508	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62347029	0.83[AMR][1000 genomes]
rs6817154	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6852279	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7656639	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657457	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686693	0.86[EUR][1000 genomes];1.00[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	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
7	nsv517536	chr4:151199080-151199497	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2290846	ATP2B1	trans	parietal	SCAN
rs2290846	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs2290846	DCLK2	cis	parietal	SCAN
rs2290846	LRBA	cis	normal skin	skin_eQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151172800-151201600	Weak transcription	GM12878-XiMat	blood
2	chr4:151173400-151201400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:151176400-151202800	Weak transcription	Psoas Muscle	Psoas
4	chr4:151178200-151204200	Weak transcription	Colonic Mucosa	Colon
5	chr4:151178400-151201400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:151178400-151201600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:151178400-151208600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:151180400-151201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:151181400-151201800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:151181600-151202000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:151181600-151202000	Weak transcription	Fetal Kidney	kidney
12	chr4:151181600-151203400	Weak transcription	Right Ventricle	heart
13	chr4:151181800-151201600	Weak transcription	Brain Angular Gyrus	brain
14	chr4:151181800-151209000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr4:151182000-151201200	Weak transcription	Fetal Heart	heart
16	chr4:151182600-151208000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:151184800-151209200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:151185000-151202000	Weak transcription	K562	blood
19	chr4:151186200-151200800	Weak transcription	NHLF	lung
20	chr4:151186200-151208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:151186400-151204800	Weak transcription	Placenta	Placenta
22	chr4:151187600-151200400	Weak transcription	HSMM	muscle
23	chr4:151187600-151202000	Weak transcription	Left Ventricle	heart
24	chr4:151187600-151206000	Weak transcription	Dnd41	blood
25	chr4:151187800-151199400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:151187800-151200400	Weak transcription	NH-A	brain
27	chr4:151187800-151200400	Weak transcription	Osteobl	bone
28	chr4:151187800-151200600	Weak transcription	HSMMtube	muscle
29	chr4:151187800-151201400	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:151187800-151202400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:151188000-151200200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:151188000-151200200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr4:151188000-151201400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:151188600-151201400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:151189800-151200600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:151190200-151204600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr4:151190600-151201400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:151191000-151201400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
40	chr4:151191600-151200800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:151192000-151200400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:151192000-151201400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:151192400-151201000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:151192400-151232800	Weak transcription	Brain Substantia Nigra	brain
45	chr4:151193400-151208400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:151193600-151203000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:151193600-151210200	Weak transcription	HepG2	liver
48	chr4:151194400-151199400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:151195200-151201200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:151195200-151205000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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