Variant report

Variant	rs7850487
Chromosome Location	chr9:19097318-19097319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19095545..19097905-chr9:19098403..19100459,2	K562	blood:
2	chr9:19084171..19086878-chr9:19096097..19098538,2	K562	blood:
3	chr9:19095602..19097894-chr9:19377705..19380132,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10122990	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10123400	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1048169	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10811107	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10811108	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10963942	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10963961	0.84[ASN][1000 genomes]
rs1154672	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1154673	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12343169	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12380322	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13287517	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2233798	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4392990	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4394488	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4439216	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62563593	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62563594	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6475313	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7022450	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7022807	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7026281	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7037787	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7045844	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7467618	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7855423	0.82[AMR][1000 genomes]
rs7856768	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv870340	chr9:19077714-19143230	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1018947	chr9:19094894-19394712	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7850487	FAM29A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:19062000-19102200	Weak transcription	Stomach Mucosa	stomach
8	chr9:19066800-19100400	Weak transcription	Fetal Heart	heart
9	chr9:19066800-19100800	Weak transcription	Small Intestine	intestine
10	chr9:19071200-19101200	Weak transcription	Psoas Muscle	Psoas
11	chr9:19073600-19098400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:19077400-19102200	Weak transcription	Gastric	stomach
13	chr9:19079200-19099600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:19079600-19101200	Weak transcription	Ovary	ovary
15	chr9:19085400-19101200	Weak transcription	Colonic Mucosa	Colon
16	chr9:19086600-19102200	Weak transcription	Aorta	Aorta
17	chr9:19089600-19102000	Weak transcription	HSMMtube	muscle
18	chr9:19089800-19101800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:19090000-19101200	Weak transcription	Right Atrium	heart
20	chr9:19090200-19101200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:19091200-19101200	Weak transcription	Esophagus	oesophagus
22	chr9:19091600-19099600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr9:19091600-19102000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:19091800-19100800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:19091800-19102000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:19092400-19100200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr9:19092400-19100800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr9:19092400-19101200	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:19092400-19101200	Weak transcription	Fetal Brain Female	brain
30	chr9:19092600-19100800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr9:19093400-19100800	Weak transcription	Fetal Brain Male	brain
32	chr9:19093600-19100200	Weak transcription	K562	blood
33	chr9:19093600-19100400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:19093600-19100400	Weak transcription	NHEK	skin
35	chr9:19093800-19100600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:19093800-19101200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:19093800-19101200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:19093800-19101200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:19093800-19101200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:19093800-19101200	Weak transcription	Left Ventricle	heart
41	chr9:19093800-19101200	Weak transcription	Lung	lung
42	chr9:19093800-19101200	Weak transcription	Pancreas	Pancrea
43	chr9:19093800-19101200	Weak transcription	Right Ventricle	heart
44	chr9:19093800-19101200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:19093800-19101200	Weak transcription	Spleen	Spleen
46	chr9:19093800-19101200	Weak transcription	NHLF	lung
47	chr9:19093800-19101400	Weak transcription	Brain Angular Gyrus	brain
48	chr9:19093800-19101800	Weak transcription	Fetal Kidney	kidney
49	chr9:19093800-19102000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr9:19093800-19102200	Weak transcription	Brain Substantia Nigra	brain

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