Variant report

Variant	rs4317401
Chromosome Location	chr6:37022490-37022491
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:37013215..37030579-chr6:37135643..37146812,60	K562	blood:
2	chr6:37021489..37023071-chr6:37031625..37033858,2	K562	blood:
3	chr6:37013215..37030665-chr6:37134901..37148307,66	K562	blood:
4	chr6:37021556..37023509-chr6:37110976..37113167,2	MCF-7	breast:
5	chr6:37021819..37031002-chr6:37065955..37074085,20	MCF-7	breast:
6	chr6:37014868..37029815-chr6:37135131..37143827,44	MCF-7	breast:
7	chr6:37016328..37032410-chr6:37132402..37145966,91	MCF-7	breast:
8	chr6:37015361..37021664-chr6:37022049..37027809,14	K562	blood:
9	chr6:37021501..37023622-chr6:37068699..37070344,2	K562	blood:
10	chr6:37005187..37007836-chr6:37021665..37024066,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1224487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1224488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1224491	0.98[ASN][1000 genomes]
rs1228575	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724094	0.98[ASN][1000 genomes]
rs1753300	0.83[ASN][1000 genomes]
rs1753301	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025998	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094575	0.86[ASN][1000 genomes]
rs2149336	0.83[ASN][1000 genomes]
rs4711482	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457976	0.85[ASN][1000 genomes]
rs6457978	0.86[ASN][1000 genomes]
rs6457979	0.82[ASN][1000 genomes]
rs6457980	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6924660	0.86[ASN][1000 genomes]
rs6939869	0.92[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748291	0.85[ASN][1000 genomes]
rs7750403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7750614	0.86[ASN][1000 genomes]
rs7750717	0.86[ASN][1000 genomes]
rs7751821	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7770544	0.83[ASN][1000 genomes]
rs831484	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831487	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831489	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831491	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs831497	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs831499	0.97[ASN][1000 genomes]
rs831500	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs831502	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs865550	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs913499	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs913500	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[ASN][1000 genomes]
rs913501	0.83[ASN][1000 genomes]
rs9296207	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296208	0.86[ASN][1000 genomes]
rs9366927	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[ASN][1000 genomes]
rs9380637	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394401	0.85[ASN][1000 genomes]
rs9394402	0.81[ASN][1000 genomes]
rs9394403	0.81[ASN][1000 genomes]
rs9462258	0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4317401	RNF8	cis	parietal	SCAN

Chromatin state (count:61 , 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	chr6:37019800-37022800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:37019800-37023000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:37019800-37023800	Weak transcription	Gastric	stomach
6	chr6:37019800-37025600	Weak transcription	NHDF-Ad	bronchial
7	chr6:37019800-37026000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:37019800-37027000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:37019800-37027200	Weak transcription	Brain Germinal Matrix	brain
10	chr6:37019800-37027200	Weak transcription	Lung	lung
11	chr6:37019800-37027200	Weak transcription	Ovary	ovary
12	chr6:37019800-37027200	Weak transcription	Right Atrium	heart
13	chr6:37020000-37022800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:37020000-37023000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:37020000-37023400	Weak transcription	Fetal Heart	heart
16	chr6:37020000-37023800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:37020000-37025400	Weak transcription	Pancreas	Pancrea
18	chr6:37020000-37027200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:37020200-37022600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:37020200-37022800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:37020200-37023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:37020200-37023200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:37020200-37023600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr6:37020200-37023800	Weak transcription	Hela-S3	cervix
25	chr6:37020200-37025400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:37020200-37027000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:37020200-37027000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:37020200-37027200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:37020200-37027200	Weak transcription	Spleen	Spleen
30	chr6:37020400-37022800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:37020400-37022800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:37020400-37023000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:37020400-37023000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:37020400-37023000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:37020400-37023000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:37020400-37023000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:37020400-37023000	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:37020400-37023200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:37020400-37023600	Weak transcription	Primary B cells from cord blood	blood
40	chr6:37020400-37023800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:37020400-37023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:37020400-37023800	Weak transcription	Placenta	Placenta
43	chr6:37020400-37024000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:37020400-37027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:37020400-37027200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:37020400-37027200	Enhancers	HepG2	liver
47	chr6:37020400-37027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:37020600-37022800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:37020600-37023000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr6:37021000-37024000	Enhancers	K562	blood

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