Variant report

Variant	rs7312638
Chromosome Location	chr12:117184484-117184485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10774885	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11068163	1.00[CHB][hapmap]
rs11068169	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1532395	0.93[ASW][hapmap];1.00[CHB][hapmap];0.90[LWK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16946979	1.00[JPT][hapmap]
rs17500871	1.00[JPT][hapmap]
rs180305	1.00[CHB][hapmap]
rs1969017	0.80[EUR][1000 genomes]
rs2644692	1.00[CHB][hapmap]
rs339448	1.00[CHB][hapmap]
rs339449	1.00[CHB][hapmap]
rs339454	1.00[CHB][hapmap]
rs339455	1.00[CHB][hapmap]
rs339456	1.00[CHB][hapmap]
rs339458	1.00[CHB][hapmap]
rs4767443	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7134604	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300541	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301614	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1048004	chr12:117170738-117219076	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv1039046	chr12:117170989-117225635	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7312638	PILRA	trans	lymphoblastoid	seeQTL
rs7312638	ABCB4	trans	lymphoblastoid	seeQTL
rs7312638	PALLD	trans	lymphoblastoid	seeQTL
rs7312638	RFC5	cis	parietal	SCAN
rs7312638	CUX2	cis	parietal	SCAN
rs7312638	TNFAIP6	trans	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117176600-117197600	Weak transcription	Aorta	Aorta
2	chr12:117176600-117197800	Weak transcription	Right Atrium	heart
3	chr12:117176800-117197600	Weak transcription	Thymus	Thymus
4	chr12:117176800-117217400	Weak transcription	Primary T cells from cord blood	blood
5	chr12:117177000-117187800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:117177000-117209400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:117177000-117217400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:117177000-117224400	Weak transcription	Brain Substantia Nigra	brain
9	chr12:117177200-117197600	Weak transcription	A549	lung
10	chr12:117177200-117216800	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:117177200-117221000	Weak transcription	Fetal Brain Male	brain
12	chr12:117177400-117225800	Weak transcription	HepG2	liver
13	chr12:117177600-117217000	Weak transcription	GM12878-XiMat	blood
14	chr12:117178000-117185600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:117178000-117194400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:117178200-117188000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:117179000-117191600	Weak transcription	Primary B cells from cord blood	blood
18	chr12:117179000-117197200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:117179000-117197600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:117179000-117217200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:117179400-117187400	Weak transcription	Brain Anterior Caudate	brain
22	chr12:117179400-117187600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:117179400-117188000	Weak transcription	Brain Angular Gyrus	brain
24	chr12:117179400-117191400	Weak transcription	Dnd41	blood
25	chr12:117179600-117198800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:117179800-117191800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:117180400-117188000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:117180800-117197400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:117181600-117186600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:117181600-117194200	Strong transcription	Fetal Brain Female	brain
31	chr12:117181800-117188200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:117182200-117185400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:117182200-117190000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:117182400-117185400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:117182600-117187800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:117182600-117187800	Weak transcription	Fetal Thymus	thymus
37	chr12:117182800-117197800	Weak transcription	Fetal Stomach	stomach
38	chr12:117182800-117198000	Weak transcription	Fetal Muscle Leg	muscle
39	chr12:117183400-117191600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:117183400-117191800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:117184000-117184600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:117184000-117184600	Enhancers	Brain Germinal Matrix	brain
43	chr12:117184000-117187000	Weak transcription	H1 Cell Line	embryonic stem cell

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