Variant report

Variant	rs12231335
Chromosome Location	chr12:42862108-42862109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42856522..42859149-chr12:42861270..42865700,4	K562	blood:
2	chr12:42851425..42853056-chr12:42860476..42863154,2	MCF-7	breast:
3	chr12:42763652..42765251-chr12:42861680..42863828,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1043652	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1043656	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880279	0.95[CEU][hapmap]
rs10880282	0.80[EUR][1000 genomes]
rs10880284	0.91[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs11181421	0.82[EUR][1000 genomes]
rs11181427	0.87[EUR][1000 genomes]
rs11181453	0.88[EUR][1000 genomes]
rs11181461	0.87[JPT][hapmap]
rs11181484	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12229224	0.85[EUR][1000 genomes]
rs12229266	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230583	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12422938	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12423383	0.91[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs12425945	0.91[CEU][hapmap]
rs12578312	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs1376931	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs1629725	0.89[EUR][1000 genomes]
rs1669884	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1669888	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1669890	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1669891	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1669894	0.89[EUR][1000 genomes]
rs1669895	0.89[EUR][1000 genomes]
rs1669897	0.89[EUR][1000 genomes]
rs1669898	0.89[EUR][1000 genomes]
rs1669899	0.87[EUR][1000 genomes]
rs1669900	0.89[EUR][1000 genomes]
rs1669901	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1669903	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1669905	0.89[EUR][1000 genomes]
rs1669911	0.88[EUR][1000 genomes]
rs1669912	0.89[EUR][1000 genomes]
rs1669913	0.89[EUR][1000 genomes]
rs1669914	0.89[EUR][1000 genomes]
rs1669935	0.89[EUR][1000 genomes]
rs1669937	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs1796354	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1796355	0.89[EUR][1000 genomes]
rs1796356	0.89[EUR][1000 genomes]
rs1796357	0.91[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1796359	0.88[EUR][1000 genomes]
rs1796360	0.88[EUR][1000 genomes]
rs1796365	0.89[EUR][1000 genomes]
rs1796373	0.89[EUR][1000 genomes]
rs1796374	0.89[EUR][1000 genomes]
rs1796377	0.89[EUR][1000 genomes]
rs1796379	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1796385	0.89[EUR][1000 genomes]
rs1796387	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796389	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796392	0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1796395	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1796396	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1796397	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1796398	0.91[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2053946	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243465	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2406872	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406969	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2600911	0.89[EUR][1000 genomes]
rs2600912	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2600916	0.89[EUR][1000 genomes]
rs2600918	0.89[EUR][1000 genomes]
rs2708063	0.89[EUR][1000 genomes]
rs2708069	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708075	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708077	0.84[EUR][1000 genomes]
rs2708506	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2952653	0.89[EUR][1000 genomes]
rs3213989	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747563	0.94[EUR][1000 genomes]
rs3761677	0.91[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs3827524	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs4603368	0.87[EUR][1000 genomes]
rs4768397	0.86[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs4768398	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs4768401	0.91[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs4768412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7134895	0.95[CEU][hapmap];0.80[JPT][hapmap];0.89[EUR][1000 genomes]
rs721447	0.88[EUR][1000 genomes]
rs73122408	0.88[EUR][1000 genomes]
rs73122414	0.88[EUR][1000 genomes]
rs73122418	0.88[EUR][1000 genomes]
rs752767	0.89[EUR][1000 genomes]
rs896555	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs896556	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12231335	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42816800-42862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
3	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
4	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
5	chr12:42837200-42863200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:42841600-42862400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:42843000-42862400	Weak transcription	Fetal Thymus	thymus
8	chr12:42843600-42862400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:42844800-42862600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:42849400-42864800	Strong transcription	Fetal Stomach	stomach
11	chr12:42850000-42866400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:42850200-42862800	Strong transcription	NH-A	brain
13	chr12:42850200-42865000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:42850200-42865000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:42850200-42865800	Strong transcription	Osteobl	bone
16	chr12:42851800-42863000	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:42852600-42862400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:42852800-42862800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:42853400-42869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:42854000-42862400	Weak transcription	Brain Anterior Caudate	brain
21	chr12:42854000-42863600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:42854000-42865800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:42854000-42868600	Weak transcription	Right Ventricle	heart
24	chr12:42854200-42865200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:42854200-42867400	Weak transcription	NHLF	lung
26	chr12:42854400-42864800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:42854400-42865200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr12:42854600-42864800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr12:42855200-42864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:42855400-42864000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:42855400-42865200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:42856200-42865800	Strong transcription	HMEC	breast
33	chr12:42856400-42863400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:42856400-42864200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:42856800-42864000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:42857000-42863000	Weak transcription	Right Atrium	heart
37	chr12:42857800-42863400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:42857800-42863800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:42858600-42862400	Strong transcription	HUVEC	blood vessel
40	chr12:42859000-42862400	Weak transcription	K562	blood
41	chr12:42859000-42863200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:42859200-42863000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:42859200-42864800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:42859200-42865200	Weak transcription	Fetal Intestine Small	intestine
45	chr12:42859600-42862200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:42859600-42862200	Weak transcription	Fetal Brain Female	brain
47	chr12:42859800-42862200	Weak transcription	Fetal Kidney	kidney
48	chr12:42859800-42862200	Weak transcription	Placenta	Placenta
49	chr12:42859800-42862400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:42859800-42862600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links