Variant report

Variant	rs183908
Chromosome Location	chr6:4965837-4965838
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1246940	0.92[ASN][1000 genomes]
rs1246941	0.89[ASN][1000 genomes]
rs1246942	1.00[CHB][hapmap]
rs1246951	1.00[CHB][hapmap]
rs1246952	1.00[CHB][hapmap]
rs169308	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1749143	0.91[CHB][hapmap]
rs1749145	0.91[CHB][hapmap]
rs1749147	0.91[CHB][hapmap]
rs275233	1.00[CHB][hapmap]
rs275235	1.00[CHB][hapmap]
rs275239	1.00[CHB][hapmap]
rs275240	1.00[CHB][hapmap]
rs275241	1.00[CHB][hapmap]
rs275242	1.00[CHB][hapmap]
rs275244	1.00[CHB][hapmap]
rs275248	1.00[CHB][hapmap]
rs275252	1.00[CHB][hapmap]
rs275253	1.00[CHB][hapmap]
rs439795	0.91[CHB][hapmap]
rs563620	0.92[CHB][hapmap]
rs808733	1.00[CHB][hapmap]

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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs183908	RPP40	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4943600-4970000	Weak transcription	Psoas Muscle	Psoas
2	chr6:4946200-4970800	Weak transcription	Fetal Brain Female	brain
3	chr6:4947600-4970600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:4954400-4967200	Weak transcription	Gastric	stomach
5	chr6:4954800-4973800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:4956800-4968000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:4956800-4970800	Weak transcription	HSMMtube	muscle
8	chr6:4957000-4970800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:4958400-4973800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:4964400-4966400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:4964400-4966600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:4964600-4966400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr6:4964800-4966000	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr6:4965000-4966400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:4965000-4966400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:4965200-4966000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:4965200-4966200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr6:4965200-4966200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:4965200-4966600	Enhancers	Stomach Smooth Muscle	stomach
20	chr6:4965400-4966000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:4965600-4966000	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:4965600-4970600	Weak transcription	Fetal Brain Male	brain
23	chr6:4965800-4966000	Enhancers	Fetal Stomach	stomach
24	chr6:4965800-4966200	Enhancers	Rectal Smooth Muscle	rectum

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