Variant report

Variant	rs7042747
Chromosome Location	chr9:3530375-3530376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:3505495..3510523-chr9:3529335..3535947,8	K562	blood:
2	chr9:3474241..3476726-chr9:3530164..3531864,2	K562	blood:

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10115088	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10118702	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10758299	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10814208	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10814219	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10814233	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10814235	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10814250	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10814251	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10972435	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10972438	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1133463	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133467	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12684702	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2027089	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3954945	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7022948	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7027862	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7041399	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7045092	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7847562	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7858486	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7864107	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7867083	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7871094	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7871777	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873538	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9774864	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9792451	0.89[EUR][1000 genomes];0.94[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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3527400-3532200	Weak transcription	Lung	lung
2	chr9:3527400-3535000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:3527400-3567600	Weak transcription	Ovary	ovary
4	chr9:3527600-3530600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:3527600-3530600	Weak transcription	Gastric	stomach
6	chr9:3527600-3532200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:3527600-3532200	Weak transcription	Placenta	Placenta
8	chr9:3527600-3534600	Weak transcription	Pancreas	Pancrea
9	chr9:3527800-3534000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:3528000-3531000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:3528000-3531400	Weak transcription	Osteobl	bone
12	chr9:3528000-3532200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:3528000-3532200	Weak transcription	NHLF	lung
14	chr9:3528000-3532800	Weak transcription	NHDF-Ad	bronchial
15	chr9:3528000-3535000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:3528000-3536000	Weak transcription	Brain Substantia Nigra	brain
17	chr9:3528000-3536200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:3528200-3531400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:3528200-3531600	Weak transcription	Fetal Lung	lung
20	chr9:3528200-3532200	Weak transcription	Fetal Stomach	stomach
21	chr9:3528200-3532400	Weak transcription	Aorta	Aorta
22	chr9:3528200-3532600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:3528200-3541200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:3528200-3550400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:3528400-3531200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:3528600-3530800	Weak transcription	NH-A	brain
27	chr9:3528600-3531000	Weak transcription	Fetal Kidney	kidney
28	chr9:3528600-3531600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:3528600-3532800	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:3528600-3534400	Weak transcription	Fetal Intestine Large	intestine
31	chr9:3528600-3535000	Weak transcription	Fetal Intestine Small	intestine
32	chr9:3528600-3554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:3528800-3530600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr9:3528800-3531400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:3528800-3531800	Weak transcription	Fetal Thymus	thymus
36	chr9:3528800-3531800	Weak transcription	NHEK	skin
37	chr9:3528800-3532600	Weak transcription	Left Ventricle	heart
38	chr9:3528800-3533000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr9:3528800-3533000	Weak transcription	Psoas Muscle	Psoas
40	chr9:3528800-3533600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:3528800-3534200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr9:3528800-3535000	Weak transcription	Small Intestine	intestine
43	chr9:3528800-3536200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:3528800-3553600	Weak transcription	Adipose Nuclei	Adipose
45	chr9:3528800-3560600	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:3529000-3531200	Strong transcription	HSMM	muscle
47	chr9:3529000-3531600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr9:3529000-3531600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr9:3529000-3532600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:3529000-3533800	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links