Variant report

Variant	rs6977512
Chromosome Location	chr7:39505059-39505060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38836202..38837177-chr7:39504337..39505154,4	K562	blood:
2	chr7:38836232..38836866-chr7:39504695..39505205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006715	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10239968	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs10268273	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1155269	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12112809	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2073540	0.89[ASW][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2073544	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2108719	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs2108720	0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.80[MKK][hapmap]
rs2159154	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2190888	0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs2190891	0.81[LWK][hapmap]
rs2237368	0.81[AFR][1000 genomes]
rs2237370	0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap]
rs2237371	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2237372	0.81[AFR][1000 genomes]
rs2237378	0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.80[MKK][hapmap]
rs2237380	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2237381	0.82[AFR][1000 genomes]
rs2237382	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2237383	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2282916	0.81[AFR][1000 genomes]
rs2282917	0.82[CHB][hapmap]
rs2282918	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2299123	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2299126	0.82[AFR][1000 genomes]
rs2302123	0.89[ASW][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs2876836	0.81[AFR][1000 genomes]
rs2876837	0.82[CHB][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs7797301	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs887014	0.82[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv966782	chr7:39454992-39581886	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6977512	C7orf36	cis	parietal	SCAN
rs6977512	ACTR2	trans	cerebellum	SCAN
rs6977512	CDK13	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39502600-39508000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:39503400-39505400	Enhancers	Primary hematopoietic stem cells	blood
3	chr7:39504000-39505200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:39504000-39505800	Enhancers	Fetal Thymus	thymus
5	chr7:39504200-39505200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr7:39504200-39508400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:39504400-39505200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:39504400-39505200	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr7:39504600-39507800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr7:39504800-39505200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:39504800-39505200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr7:39504800-39505200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:39504800-39505200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:39504800-39505200	Flanking Active TSS	Liver	Liver
15	chr7:39504800-39505200	Enhancers	Fetal Lung	lung
16	chr7:39504800-39505200	Enhancers	Thymus	Thymus
17	chr7:39504800-39505200	Flanking Active TSS	A549	lung
18	chr7:39504800-39505200	Flanking Bivalent TSS/Enh	HepG2	liver
19	chr7:39504800-39505200	Active TSS	NHDF-Ad	bronchial
20	chr7:39504800-39505400	Enhancers	Fetal Brain Male	brain
21	chr7:39504800-39506000	Enhancers	Dnd41	blood
22	chr7:39505000-39505200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr7:39505000-39505200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr7:39505000-39505200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:39505000-39505200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:39505000-39505200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:39505000-39505200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr7:39505000-39505200	Bivalent Enhancer	HSMMtube	muscle
29	chr7:39505000-39505200	Active TSS	K562	blood
30	chr7:39505000-39507800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:39505000-39508400	Weak transcription	Fetal Muscle Leg	muscle
32	chr7:39505000-39512800	Weak transcription	Fetal Kidney	kidney

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