Variant report

Variant	rs913500
Chromosome Location	chr6:37025436-37025437
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37025219..37028736-chr6:37042673..37044927,4	MCF-7	breast:
2	chr6:37013215..37030579-chr6:37135643..37146812,60	K562	blood:
3	chr6:37023226..37025868-chr6:37041331..37043544,2	K562	blood:
4	chr6:37022707..37025816-chr6:37101258..37104002,3	MCF-7	breast:
5	chr6:36995831..36998687-chr6:37024606..37026177,2	K562	blood:
6	chr6:37013215..37030665-chr6:37134901..37148307,66	K562	blood:
7	chr6:37022535..37025870-chr6:37027364..37029356,3	K562	blood:
8	chr6:36993908..36995682-chr6:37024322..37026028,2	MCF-7	breast:
9	chr6:37021819..37031002-chr6:37065955..37074085,20	MCF-7	breast:
10	chr6:37014868..37029815-chr6:37135131..37143827,44	MCF-7	breast:
11	chr6:37023016..37028102-chr6:37100867..37105079,9	MCF-7	breast:
12	chr6:37016328..37032410-chr6:37132402..37145966,91	MCF-7	breast:
13	chr6:37015361..37021664-chr6:37022049..37027809,14	K562	blood:
14	chr6:37024224..37026313-chr6:37036229..37037953,2	MCF-7	breast:
15	chr6:37019826..37021795-chr6:37024868..37026778,2	MCF-7	breast:
16	chr6:36995831..36998687-chr6:37023860..37026177,3	K562	blood:
17	chr6:37024053..37026125-chr6:37149317..37151146,2	K562	blood:
18	chr6:37024864..37027395-chr6:37049867..37052313,2	K562	blood:
19	chr6:37025139..37026735-chr6:37035518..37038380,2	K562	blood:
20	chr6:37025397..37029627-chr6:37037607..37042418,9	MCF-7	breast:
21	chr20:45986965..45989735-chr6:37024564..37027465,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1224487	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1224488	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1224491	0.91[ASN][1000 genomes]
rs1228575	0.93[ASN][1000 genomes]
rs1724094	0.91[ASN][1000 genomes]
rs1753301	0.93[ASN][1000 genomes]
rs2025998	0.93[ASN][1000 genomes]
rs2094575	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2149336	0.83[ASN][1000 genomes]
rs4317401	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[ASN][1000 genomes]
rs4711482	0.93[ASN][1000 genomes]
rs6457974	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[ASN][1000 genomes]
rs6457976	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6457978	0.86[ASN][1000 genomes]
rs6457979	0.85[ASN][1000 genomes]
rs6457980	0.85[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs6924660	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6939869	0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7748291	0.88[ASN][1000 genomes]
rs7750403	0.88[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7750614	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7750717	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7751821	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7770544	0.83[ASN][1000 genomes]
rs7774073	0.80[ASN][1000 genomes]
rs831484	0.93[ASN][1000 genomes]
rs831487	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs831489	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs831491	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs831497	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs831499	0.90[ASN][1000 genomes]
rs831500	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs831502	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs913499	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs9296207	0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9296208	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9366927	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380637	0.82[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs9394401	0.85[ASN][1000 genomes]
rs9394402	0.85[ASN][1000 genomes]
rs9394403	0.82[ASN][1000 genomes]
rs9462258	0.82[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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs913500	RNF8	cis	parietal	SCAN
rs913500	FGD2	cis	multi-tissue	Pritchard

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37017200-37027200	Weak transcription	NH-A	brain
2	chr6:37019600-37025800	Weak transcription	HSMM	muscle
3	chr6:37019800-37025600	Weak transcription	NHDF-Ad	bronchial
4	chr6:37019800-37026000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:37019800-37027000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:37019800-37027200	Weak transcription	Brain Germinal Matrix	brain
7	chr6:37019800-37027200	Weak transcription	Lung	lung
8	chr6:37019800-37027200	Weak transcription	Ovary	ovary
9	chr6:37019800-37027200	Weak transcription	Right Atrium	heart
10	chr6:37020000-37027200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:37020200-37027000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:37020200-37027000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:37020200-37027200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:37020200-37027200	Weak transcription	Spleen	Spleen
15	chr6:37020400-37027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:37020400-37027200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:37020400-37027200	Enhancers	HepG2	liver
18	chr6:37020400-37027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:37021400-37026600	Weak transcription	Fetal Intestine Small	intestine
20	chr6:37022600-37026400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:37022800-37026000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:37023000-37025800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:37023000-37026200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:37023200-37027000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:37023800-37026200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:37023800-37027200	Enhancers	Hela-S3	cervix
27	chr6:37024000-37027200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:37024000-37027200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:37024000-37027200	Weak transcription	Fetal Heart	heart
30	chr6:37024400-37025800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:37024400-37026000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:37024400-37026000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:37024400-37026600	Weak transcription	Stomach Mucosa	stomach
34	chr6:37024400-37027000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:37024400-37027400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:37024400-37027600	Weak transcription	Fetal Thymus	thymus
37	chr6:37024400-37028400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr6:37024600-37026200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:37024600-37026400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:37024600-37027000	Weak transcription	Primary B cells from cord blood	blood
41	chr6:37024600-37027200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr6:37024600-37027200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:37024600-37027400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:37024600-37029000	Weak transcription	Gastric	stomach
45	chr6:37024800-37025800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:37024800-37026400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:37024800-37027200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:37024800-37027200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:37024800-37027200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:37024800-37027200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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