Variant report

Variant	rs4696660
Chromosome Location	chr4:151191830-151191831
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10520053	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1080195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs11722135	0.82[CHB][hapmap]
rs11728745	0.83[CHB][hapmap]
rs11734677	0.89[GIH][hapmap]
rs11734774	0.83[AMR][1000 genomes]
rs1507190	0.83[CHB][hapmap];0.83[AMR][1000 genomes]
rs1507191	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs17503902	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17503964	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs17504117	0.83[AMR][1000 genomes]
rs17588356	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17588629	0.80[AMR][1000 genomes]
rs1824406	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056457	0.83[CHB][hapmap];0.83[AMR][1000 genomes]
rs2085722	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290846	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749574	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696646	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55728314	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55889963	0.83[AMR][1000 genomes]
rs56169929	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58138000	0.83[AMR][1000 genomes]
rs59435073	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59713336	0.80[AMR][1000 genomes]
rs60459852	0.80[AMR][1000 genomes]
rs62344508	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62346985	0.80[AMR][1000 genomes]
rs62346990	0.82[AMR][1000 genomes]
rs6816533	0.83[AFR][1000 genomes]
rs6817154	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834124	0.80[AMR][1000 genomes]
rs6841587	0.81[AFR][1000 genomes]
rs6852279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72734403	0.83[AMR][1000 genomes]
rs7656639	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657457	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686693	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4696660	ATP2B1	trans	parietal	SCAN
rs4696660	DCLK2	cis	parietal	SCAN
rs4696660	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151166400-151199000	Weak transcription	Gastric	stomach
2	chr4:151170000-151199000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:151172800-151201600	Weak transcription	GM12878-XiMat	blood
4	chr4:151173200-151192000	Weak transcription	Fetal Brain Male	brain
5	chr4:151173400-151201400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:151176400-151202800	Weak transcription	Psoas Muscle	Psoas
7	chr4:151178000-151193200	Weak transcription	Fetal Lung	lung
8	chr4:151178200-151192800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:151178200-151193000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:151178200-151204200	Weak transcription	Colonic Mucosa	Colon
11	chr4:151178400-151192800	Weak transcription	Lung	lung
12	chr4:151178400-151201400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:151178400-151201600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:151178400-151208600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:151180000-151198800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:151180200-151197800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:151180400-151201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:151181200-151195400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:151181400-151193000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:151181400-151198800	Weak transcription	Spleen	Spleen
21	chr4:151181400-151201800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:151181600-151198600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:151181600-151202000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:151181600-151202000	Weak transcription	Fetal Kidney	kidney
25	chr4:151181600-151203400	Weak transcription	Right Ventricle	heart
26	chr4:151181800-151201600	Weak transcription	Brain Angular Gyrus	brain
27	chr4:151181800-151209000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:151182000-151198800	Weak transcription	Esophagus	oesophagus
29	chr4:151182000-151201200	Weak transcription	Fetal Heart	heart
30	chr4:151182600-151208000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:151182800-151193000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:151183000-151192000	Weak transcription	Fetal Stomach	stomach
33	chr4:151184600-151192000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:151184600-151199000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:151184800-151209200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:151185000-151192000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:151185000-151202000	Weak transcription	K562	blood
38	chr4:151186200-151198200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:151186200-151200800	Weak transcription	NHLF	lung
40	chr4:151186200-151208000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr4:151186400-151204800	Weak transcription	Placenta	Placenta
42	chr4:151187200-151199000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr4:151187400-151198800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:151187600-151192000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:151187600-151192000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:151187600-151192000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:151187600-151192200	Weak transcription	Pancreas	Pancrea
48	chr4:151187600-151192600	Weak transcription	Aorta	Aorta
49	chr4:151187600-151192800	Weak transcription	Brain Anterior Caudate	brain
50	chr4:151187600-151192800	Weak transcription	Fetal Muscle Trunk	muscle

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