Variant report

Variant	rs7871777
Chromosome Location	chr9:3529411-3529412
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:3520146-3530139	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:3523584-3529804	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:3525215-3529421	PBDE	blood:	n/a	n/a
4	TBL1XR1	chr9:3528402-3529676	K562	blood:	n/a	n/a
5	POLR2A	chr9:3525692-3530126	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:3488422..3492745-chr9:3526119..3529756,3	K562	blood:
2	chr9:2841657..2846061-chr9:3525153..3529600,6	K562	blood:
3	chr9:3498806..3500362-chr9:3527236..3529774,2	K562	blood:
4	chr9:3505495..3510523-chr9:3529335..3535947,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNV2-3	chr9:3526119-3532720	NONHSAT130021

No data

Variant related genes	Relation type
RFX3	TF binding region
ENSG00000080608	Chromatin interaction
ENSG00000080298	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10114162	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs10114838	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs10115088	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10115578	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs10118702	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119982	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs10121096	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs10758299	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10814189	0.91[JPT][hapmap]
rs10814190	0.90[JPT][hapmap]
rs10814208	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10814219	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10814233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10814235	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10814250	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10814251	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10972435	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10972438	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133463	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133467	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12004862	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs12238307	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs12340274	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs12353393	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs12684702	0.88[ASN][1000 genomes]
rs1342542	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs2027089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28510559	0.81[EUR][1000 genomes]
rs3954945	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7022948	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7026025	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7027862	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7041399	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7042747	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7045092	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7847562	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7857554	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7858486	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7861625	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs7864107	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7867083	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7871094	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7873538	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs881167	0.87[CEU][hapmap];0.91[JPT][hapmap]
rs9774864	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9792451	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv539944	chr9:3476471-3535344	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3522600-3530200	Active TSS	K562	blood
2	chr9:3526800-3529800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:3527000-3530200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:3527400-3532200	Weak transcription	Lung	lung
5	chr9:3527400-3535000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:3527400-3567600	Weak transcription	Ovary	ovary
7	chr9:3527600-3530600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:3527600-3530600	Weak transcription	Gastric	stomach
9	chr9:3527600-3532200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:3527600-3532200	Weak transcription	Placenta	Placenta
11	chr9:3527600-3534600	Weak transcription	Pancreas	Pancrea
12	chr9:3527800-3534000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:3528000-3531000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:3528000-3531400	Weak transcription	Osteobl	bone
15	chr9:3528000-3532200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:3528000-3532200	Weak transcription	NHLF	lung
17	chr9:3528000-3532800	Weak transcription	NHDF-Ad	bronchial
18	chr9:3528000-3535000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:3528000-3536000	Weak transcription	Brain Substantia Nigra	brain
20	chr9:3528000-3536200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:3528200-3531400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:3528200-3531600	Weak transcription	Fetal Lung	lung
23	chr9:3528200-3532200	Weak transcription	Fetal Stomach	stomach
24	chr9:3528200-3532400	Weak transcription	Aorta	Aorta
25	chr9:3528200-3532600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:3528200-3541200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:3528200-3550400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:3528400-3531200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:3528600-3530200	Enhancers	HepG2	liver
30	chr9:3528600-3530800	Weak transcription	NH-A	brain
31	chr9:3528600-3531000	Weak transcription	Fetal Kidney	kidney
32	chr9:3528600-3531600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:3528600-3532800	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:3528600-3534400	Weak transcription	Fetal Intestine Large	intestine
35	chr9:3528600-3535000	Weak transcription	Fetal Intestine Small	intestine
36	chr9:3528600-3554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:3528800-3529800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:3528800-3530200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:3528800-3530600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:3528800-3531400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:3528800-3531800	Weak transcription	Fetal Thymus	thymus
42	chr9:3528800-3531800	Weak transcription	NHEK	skin
43	chr9:3528800-3532600	Weak transcription	Left Ventricle	heart
44	chr9:3528800-3533000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr9:3528800-3533000	Weak transcription	Psoas Muscle	Psoas
46	chr9:3528800-3533600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr9:3528800-3534200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:3528800-3535000	Weak transcription	Small Intestine	intestine
49	chr9:3528800-3536200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr9:3528800-3553600	Weak transcription	Adipose Nuclei	Adipose

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