Variant report

Variant	rs6477997
Chromosome Location	chr9:115981113-115981114
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:115980360..115986264-chr9:116170629..116175189,6	K562	blood:
2	chr9:115975066..115976588-chr9:115978815..115981431,2	MCF-7	breast:
3	chr9:115981081..115983502-chr9:115983537..115987172,3	MCF-7	breast:
4	chr9:115979802..115981343-chr9:115983049..115985677,2	K562	blood:
5	chr9:115978706..115980364-chr9:115981064..115982891,2	K562	blood:
6	chr9:115974346..115976683-chr9:115980205..115982463,2	MCF-7	breast:
7	chr9:115979271..115982033-chr9:115982056..115983606,2	MCF-7	breast:
8	chr9:115949400..115951556-chr9:115979789..115982738,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157653	Chromatin interaction
ENSG00000136868	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000119321	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10081797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114381	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10114423	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10116039	0.82[GIH][hapmap]
rs10121845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739389	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739391	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759631	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759635	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817460	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817465	0.88[ASW][hapmap];0.87[GIH][hapmap];0.89[YRI][hapmap]
rs10817470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338001	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979224	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851623	0.84[CEU][hapmap]
rs7855694	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6477997	SVEP1	cis	parietal	SCAN
rs6477997	PRPF4	cis	Thyroid	GTEx
rs6477997	ZNF618	cis	cerebellum	SCAN
rs6477997	CDC26	cis	parietal	SCAN
rs6477997	CDC26	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115936800-115982400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:115950600-115982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:115951000-115982800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:115965200-115982000	Weak transcription	Colonic Mucosa	Colon
7	chr9:115965200-115982000	Weak transcription	Fetal Brain Male	brain
8	chr9:115965200-115982200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:115969000-115982400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:115969400-115981800	Weak transcription	HSMM	muscle
11	chr9:115969600-115981600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:115969600-115982400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:115969600-115982400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:115970000-115982800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:115970400-115981800	Weak transcription	NH-A	brain
16	chr9:115970600-115981800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:115971600-115982000	Weak transcription	NHDF-Ad	bronchial
18	chr9:115971800-115982000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:115972400-115981200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:115972400-115981200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:115972400-115981600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:115972600-115981600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr9:115972600-115981800	Weak transcription	HMEC	breast
24	chr9:115972600-115982800	Weak transcription	Gastric	stomach
25	chr9:115972800-115981800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:115972800-115982000	Weak transcription	HSMMtube	muscle
27	chr9:115973200-115981800	Weak transcription	Fetal Kidney	kidney
28	chr9:115973200-115981800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:115973200-115982000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:115973200-115982000	Weak transcription	A549	lung
31	chr9:115973200-115982400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr9:115973200-115982400	Weak transcription	Spleen	Spleen
33	chr9:115973200-115982600	Weak transcription	Ovary	ovary
34	chr9:115973400-115981800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:115973400-115981800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:115973400-115981800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:115973400-115981800	Weak transcription	Thymus	Thymus
38	chr9:115973400-115981800	Weak transcription	NHLF	lung
39	chr9:115973400-115982000	Weak transcription	Fetal Lung	lung
40	chr9:115973400-115982000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:115973400-115982200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:115973400-115982200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:115973400-115982400	Weak transcription	Esophagus	oesophagus
44	chr9:115973400-115982400	Weak transcription	Pancreas	Pancrea
45	chr9:115973600-115981600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:115973800-115981200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:115973800-115981800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:115973800-115981800	Weak transcription	Right Ventricle	heart
49	chr9:115973800-115982000	Weak transcription	Aorta	Aorta
50	chr9:115973800-115982200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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