Variant report

Variant	rs2346781
Chromosome Location	chr4:159068324-159068325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10008208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012339	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10028490	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645131	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648410	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs14202	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879659	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346321	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2346784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881373	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4234917	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4309890	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4317248	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4345228	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4501266	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691455	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691461	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6536299	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6820988	1.00[ASN][1000 genomes]
rs6830702	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6833198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852878	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8370	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2346781	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs2346781	RP11-597D13.7	cis	Nerve Tibial	GTEx
rs2346781	RP11-597D13.9	cis	Heart Left Ventricle	GTEx
rs2346781	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs2346781	FAM198B	cis	Whole Blood	GTEx
rs2346781	TMEM144	cis	Esophagus Muscularis	GTEx
rs2346781	TMEM144	cis	Whole Blood	GTEx
rs2346781	TMEM144	cis	Artery Aorta	GTEx
rs2346781	TMEM144	cis	Nerve Tibial	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:159044800-159071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
5	chr4:159049200-159070000	Weak transcription	Placenta	Placenta
6	chr4:159051800-159070600	Weak transcription	Fetal Intestine Large	intestine
7	chr4:159051800-159073000	Weak transcription	Fetal Stomach	stomach
8	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:159052000-159071400	Weak transcription	Adipose Nuclei	Adipose
10	chr4:159052200-159071400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:159052200-159072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:159052600-159071200	Weak transcription	Fetal Intestine Small	intestine
13	chr4:159052600-159071400	Weak transcription	HSMMtube	muscle
14	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
15	chr4:159055600-159076200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:159059000-159077800	Weak transcription	Aorta	Aorta
17	chr4:159059400-159071800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:159059400-159076600	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:159060600-159070800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:159060600-159071200	Weak transcription	Ovary	ovary
21	chr4:159060600-159071400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:159060600-159076600	Weak transcription	HMEC	breast
23	chr4:159062000-159077600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:159062600-159077800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:159062600-159083600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:159063200-159071600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:159063400-159078800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr4:159064000-159071800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:159066200-159076600	Weak transcription	Small Intestine	intestine
30	chr4:159066200-159076800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr4:159066400-159069800	Weak transcription	Fetal Heart	heart
32	chr4:159066400-159080400	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:159066600-159071400	Weak transcription	HepG2	liver
34	chr4:159066600-159072000	Weak transcription	HUVEC	blood vessel
35	chr4:159067400-159077200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:159067600-159068600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr4:159067600-159069400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:159067600-159073400	Strong transcription	HSMM	muscle
39	chr4:159067800-159068400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:159067800-159068600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr4:159067800-159068600	Enhancers	Brain Cingulate Gyrus	brain
42	chr4:159067800-159068600	Enhancers	Brain Substantia Nigra	brain
43	chr4:159067800-159068800	Enhancers	Brain Angular Gyrus	brain
44	chr4:159067800-159068800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr4:159068200-159068600	Enhancers	Brain Anterior Caudate	brain

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