Variant report

Variant	rs7657457
Chromosome Location	chr4:151210761-151210762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10520053	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080195	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11059	0.87[CEU][hapmap]
rs11722135	0.82[CHB][hapmap]
rs11728745	0.83[CHB][hapmap]
rs11734677	0.89[GIH][hapmap]
rs11734774	0.81[AMR][1000 genomes]
rs1507190	0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs1507191	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs17503902	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503964	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs17504117	0.81[AMR][1000 genomes]
rs17588356	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824406	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2056457	0.83[CHB][hapmap];0.81[AMR][1000 genomes]
rs2085722	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290846	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749574	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696646	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696651	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696659	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696660	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55728314	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55889963	0.81[AMR][1000 genomes]
rs56169929	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58138000	0.81[AMR][1000 genomes]
rs59435073	0.81[ASN][1000 genomes]
rs62344508	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62346990	0.82[AMR][1000 genomes]
rs6816533	0.81[AFR][1000 genomes]
rs6817154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852279	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72734403	0.81[AMR][1000 genomes]
rs7656639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686693	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7657457	ATP2B1	trans	parietal	SCAN
rs7657457	DCLK2	cis	parietal	SCAN
rs7657457	LRBA	Cis_1M	lymphoblastoid	RTeQTL
rs7657457	FZD3	trans	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151191400-151245200	Weak transcription	Small Intestine	intestine
2	chr4:151192400-151232800	Weak transcription	Brain Substantia Nigra	brain
3	chr4:151202200-151213200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:151202200-151218000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:151202600-151213200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:151202800-151223800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:151203600-151218400	Weak transcription	Fetal Stomach	stomach
8	chr4:151203800-151211000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:151203800-151244400	Weak transcription	Fetal Thymus	thymus
10	chr4:151204000-151211000	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:151204000-151223800	Weak transcription	K562	blood
12	chr4:151204000-151244600	Weak transcription	Lung	lung
13	chr4:151204200-151213200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:151204600-151213200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:151204600-151213600	Weak transcription	Aorta	Aorta
16	chr4:151204600-151216800	Weak transcription	Pancreas	Pancrea
17	chr4:151204600-151236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr4:151204600-151242200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:151204800-151211000	Weak transcription	Fetal Intestine Small	intestine
20	chr4:151205000-151213200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:151205000-151236400	Weak transcription	Primary B cells from cord blood	blood
22	chr4:151205000-151272200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:151205400-151212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:151206400-151213200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:151206600-151222800	Weak transcription	Osteobl	bone
26	chr4:151206800-151223800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:151206800-151223800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr4:151207200-151226600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:151207600-151241600	Weak transcription	Fetal Intestine Large	intestine
30	chr4:151208000-151230400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:151208600-151230400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr4:151209000-151211200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:151209000-151213200	Weak transcription	Primary T cells from cord blood	blood
34	chr4:151210000-151212000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:151210200-151211200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:151210200-151211200	Enhancers	HepG2	liver
37	chr4:151210400-151210800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:151210400-151211200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:151210400-151211200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr4:151210600-151210800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr4:151210600-151211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:151210600-151212000	Enhancers	Rectal Smooth Muscle	rectum

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