Variant report

Variant	rs1246940
Chromosome Location	chr6:4964891-4964892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1246941	0.88[ASN][1000 genomes]
rs1246942	0.91[CHB][hapmap]
rs1246951	0.91[CHB][hapmap]
rs1246952	0.90[CHB][hapmap]
rs1246985	0.80[CEU][hapmap]
rs1271970	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs1749143	0.81[CHB][hapmap]
rs1749145	0.82[CHB][hapmap]
rs1749147	0.82[CHB][hapmap]
rs183908	0.92[ASN][1000 genomes]
rs275233	0.91[CHB][hapmap]
rs275235	0.91[CHB][hapmap]
rs275239	0.91[CHB][hapmap]
rs275240	0.91[CHB][hapmap]
rs275241	0.91[CHB][hapmap]
rs275242	0.91[CHB][hapmap]
rs275244	0.91[CHB][hapmap]
rs275248	0.90[CHB][hapmap]
rs275252	0.91[CHB][hapmap]
rs275253	0.90[CHB][hapmap]
rs439795	0.82[CHB][hapmap]
rs563620	0.82[CHB][hapmap]
rs728151	0.81[CEU][hapmap]
rs808733	0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1246940	MUTED	cis	cerebellum	SCAN
rs1246940	RPP40	cis	lymphoblastoid	seeQTL
rs1246940	C6orf145	cis	cerebellum	SCAN

Chromatin state (count:27 , 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	chr6:4949200-4965200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:4954400-4967200	Weak transcription	Gastric	stomach
6	chr6:4954800-4965200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:4954800-4973800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:4955000-4965800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:4956600-4965000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:4956600-4965400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:4956600-4965400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:4956800-4965200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:4956800-4965200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:4956800-4965400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:4956800-4968000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:4956800-4970800	Weak transcription	HSMMtube	muscle
17	chr6:4957000-4965200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:4957000-4970800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:4958400-4965000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:4958400-4973800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:4964400-4965200	Weak transcription	Fetal Brain Male	brain
22	chr6:4964400-4966400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:4964400-4966600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:4964600-4965600	Enhancers	Colon Smooth Muscle	Colon
25	chr6:4964600-4966400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr6:4964800-4965200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr6:4964800-4966000	Flanking Bivalent TSS/Enh	HepG2	liver

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