Variant report

Variant	rs4309890
Chromosome Location	chr4:159053746-159053747
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159050755..159053105-chr4:159053356..159055470,2	MCF-7	breast:
2	chr4:159031275..159033687-chr4:159053603..159055452,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10008208	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10012339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028490	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645131	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12648410	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs14202	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879659	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346321	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2346781	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346784	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881373	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4234917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317248	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691455	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691461	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6536299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820988	0.93[ASN][1000 genomes]
rs6830702	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6833198	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6852878	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4309890	TMEM144	cis	Nerve Tibial	GTEx
rs4309890	TMEM144	cis	Esophagus Muscularis	GTEx
rs4309890	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs4309890	RP11-597D13.9	cis	Heart Left Ventricle	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain
2	chr4:159042800-159053800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:159042800-159054800	Weak transcription	Fetal Heart	heart
4	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:159044800-159071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:159045200-159058600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr4:159045200-159059400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:159046200-159054200	Strong transcription	HUVEC	blood vessel
10	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
11	chr4:159047200-159058600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:159049200-159070000	Weak transcription	Placenta	Placenta
13	chr4:159049400-159053800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:159051000-159061000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:159051600-159056000	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:159051800-159070600	Weak transcription	Fetal Intestine Large	intestine
17	chr4:159051800-159073000	Weak transcription	Fetal Stomach	stomach
18	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:159052000-159054600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:159052000-159071400	Weak transcription	Adipose Nuclei	Adipose
21	chr4:159052200-159054000	Enhancers	NHDF-Ad	bronchial
22	chr4:159052200-159054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:159052200-159055200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:159052200-159071400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:159052200-159072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:159052400-159053800	Enhancers	Small Intestine	intestine
27	chr4:159052400-159060200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:159052600-159060400	Weak transcription	Ovary	ovary
29	chr4:159052600-159071200	Weak transcription	Fetal Intestine Small	intestine
30	chr4:159052600-159071400	Weak transcription	HSMMtube	muscle
31	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
32	chr4:159052800-159053800	Weak transcription	HepG2	liver
33	chr4:159052800-159060200	Weak transcription	HMEC	breast
34	chr4:159053000-159054400	Strong transcription	HSMM	muscle
35	chr4:159053400-159053800	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:159053400-159054200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:159053400-159054200	Enhancers	Aorta	Aorta
38	chr4:159053600-159053800	Enhancers	Brain Anterior Caudate	brain
39	chr4:159053600-159054000	Weak transcription	Rectal Smooth Muscle	rectum

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