Variant report

Variant	rs10031902
Chromosome Location	chr4:152197483-152197484
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:152197359-152198508	SK-N-SH	brain:	n/a	chr4:152198095-152198113 chr4:152198098-152198111 chr4:152198100-152198110 chr4:152198097-152198118 chr4:152198096-152198112

Variant related genes	Relation type
PRSS48	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10006091	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10011948	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10012999	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10015834	0.93[EUR][1000 genomes]
rs10016704	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10019075	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10031618	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10857257	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099797	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099798	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099799	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11099802	0.95[EUR][1000 genomes]
rs11721421	0.94[EUR][1000 genomes]
rs11726496	0.95[EUR][1000 genomes]
rs11729901	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11730707	1.00[EUR][1000 genomes]
rs11733473	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11733501	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11733600	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs11734518	0.95[EUR][1000 genomes]
rs11734727	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11735681	0.94[EUR][1000 genomes]
rs12501397	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12505382	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12508449	0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17590780	0.95[EUR][1000 genomes]
rs2291978	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407166	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28650996	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28651657	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28767036	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35245353	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3990708	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs4339187	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4417949	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4473634	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55812154	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55855806	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55869644	0.95[EUR][1000 genomes]
rs55905531	0.95[EUR][1000 genomes]
rs56220030	0.93[EUR][1000 genomes]
rs62328350	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62328351	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62328353	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535780	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535781	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535782	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6535785	0.88[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs6823844	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824159	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824195	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6844983	0.98[EUR][1000 genomes]
rs6849871	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs6849875	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6851493	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72725927	0.95[EUR][1000 genomes]
rs7663659	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7665657	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7695360	0.99[EUR][1000 genomes]
rs9990564	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9994652	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9996742	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9997461	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10031902	FAM160A1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:152173800-152198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:152177400-152198200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:152182600-152211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:152182800-152206000	Weak transcription	NHEK	skin
7	chr4:152183200-152198200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:152185000-152198200	Weak transcription	Right Ventricle	heart
9	chr4:152185200-152197600	Weak transcription	Left Ventricle	heart
10	chr4:152188600-152204000	Weak transcription	Gastric	stomach
11	chr4:152189200-152197600	Weak transcription	Ovary	ovary
12	chr4:152189400-152197600	Weak transcription	Fetal Intestine Small	intestine
13	chr4:152189400-152197600	Weak transcription	HepG2	liver
14	chr4:152189400-152198200	Weak transcription	Fetal Intestine Large	intestine
15	chr4:152189400-152202400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr4:152189400-152205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:152189600-152198400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:152190800-152208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:152191200-152204200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:152192600-152197600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:152192800-152198200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:152193600-152197600	Weak transcription	Brain Substantia Nigra	brain
23	chr4:152193800-152198200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:152194000-152197600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:152194000-152198200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:152194200-152197600	Weak transcription	Stomach Mucosa	stomach
27	chr4:152194200-152197800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:152194200-152202400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:152194200-152213200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr4:152194400-152198200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:152196000-152204000	Weak transcription	Fetal Stomach	stomach
32	chr4:152196000-152218400	Weak transcription	Psoas Muscle	Psoas
33	chr4:152196200-152199600	Weak transcription	Right Atrium	heart
34	chr4:152196600-152197600	Weak transcription	Aorta	Aorta
35	chr4:152196800-152198000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr4:152197400-152198600	Enhancers	Brain Angular Gyrus	brain
37	chr4:152197400-152198800	Enhancers	Brain Hippocampus Middle	brain
38	chr4:152197400-152199200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links