Variant report

Variant	rs2473153
Chromosome Location	chr6:144633601-144633602
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2473152	0.98[ASN][1000 genomes]
rs2473154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs584283	0.85[AMR][1000 genomes]
rs586016	0.87[AMR][1000 genomes]
rs587691	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs589892	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs591311	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs592667	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs601816	0.83[EUR][1000 genomes]
rs601873	0.83[EUR][1000 genomes]
rs602764	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs603692	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs615755	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs616619	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs632972	0.80[EUR][1000 genomes]
rs633106	0.82[EUR][1000 genomes]
rs633802	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs649426	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs662419	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs664541	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs665135	0.81[AMR][1000 genomes]
rs672468	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs676859	0.84[AMR][1000 genomes]
rs681916	0.81[AMR][1000 genomes]
rs74671	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs849661	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs926397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2473153	RP1-83M4.2	cis	Nerve Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144609200-144641600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:144616400-144648000	Weak transcription	NHEK	skin
3	chr6:144617200-144636400	Weak transcription	A549	lung
4	chr6:144619200-144634600	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:144619800-144634600	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:144622400-144637000	Genic enhancers	HepG2	liver
7	chr6:144624200-144641400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:144624200-144641600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:144624400-144648000	Weak transcription	HMEC	breast
10	chr6:144627000-144634600	Weak transcription	Small Intestine	intestine
11	chr6:144627400-144634600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:144627400-144641800	Weak transcription	Thymus	Thymus
13	chr6:144627600-144634200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:144627600-144634200	Weak transcription	Right Atrium	heart
15	chr6:144627600-144634600	Weak transcription	Aorta	Aorta
16	chr6:144627600-144634600	Weak transcription	Esophagus	oesophagus
17	chr6:144627600-144634600	Weak transcription	Spleen	Spleen
18	chr6:144627600-144636400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:144627600-144643400	Weak transcription	NH-A	brain
20	chr6:144627600-144645800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:144627800-144634600	Weak transcription	Fetal Thymus	thymus
22	chr6:144629200-144634400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:144629200-144634400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:144629200-144635200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:144629400-144641800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:144630200-144648400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:144630400-144634000	Weak transcription	Right Ventricle	heart
28	chr6:144630400-144634600	Weak transcription	Gastric	stomach
29	chr6:144630600-144634200	Weak transcription	NHDF-Ad	bronchial
30	chr6:144630600-144648200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:144630800-144634200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:144630800-144634600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:144630800-144634600	Weak transcription	Placenta	Placenta
34	chr6:144630800-144634800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:144631000-144634200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr6:144631000-144634200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:144631000-144634200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:144631000-144634200	Weak transcription	Left Ventricle	heart
39	chr6:144631000-144634600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:144631000-144635600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:144631000-144636400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:144631000-144636400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr6:144631200-144634000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:144631200-144634200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:144631200-144634200	Weak transcription	HUVEC	blood vessel
46	chr6:144631200-144634200	Weak transcription	NHLF	lung
47	chr6:144631200-144634400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:144631200-144634600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:144631200-144634600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr6:144631200-144634600	Weak transcription	Fetal Stomach	stomach

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