Variant report

Variant	rs7315690
Chromosome Location	chr12:50581490-50581491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50580197..50581923-chr12:50586405..50588102,2	MCF-7	breast:
2	chr12:50581029..50583186-chr12:50589961..50592504,2	K562	blood:
3	chr12:50580926..50582458-chr12:50694588..50696573,2	K562	blood:
4	chr12:50494779..50496770-chr12:50580930..50583247,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CERS5-1	chr12:50579363-50584044	ENSG00000257298.1

Variant related genes	Relation type
ENSG00000203428	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10506292	0.96[CEU][hapmap]
rs10783338	0.83[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs10783344	0.96[CEU][hapmap]
rs10876000	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10876014	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs10876015	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs10876017	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs10876023	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs10876024	0.95[CEU][hapmap]
rs11169281	0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs11169282	0.88[ASW][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap]
rs11169314	0.81[EUR][1000 genomes]
rs11169315	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs11169322	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs11169331	0.96[CEU][hapmap]
rs11169332	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11169335	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11169348	0.96[CEU][hapmap]
rs11169350	0.96[CEU][hapmap]
rs11169351	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11169357	0.96[CEU][hapmap]
rs11169360	1.00[CEU][hapmap]
rs11169370	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs11833608	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs11838347	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12303082	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12367872	0.96[CEU][hapmap];0.80[TSI][hapmap]
rs12422417	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12424335	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12424691	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs12424713	0.96[CEU][hapmap]
rs12425705	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs12828340	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs1362983	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs1554844	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs1554845	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs17124432	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs17124514	0.84[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2111988	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs2302900	0.91[CEU][hapmap]
rs2358539	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs34245511	0.93[ASN][1000 genomes]
rs3741562	0.88[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs3812825	0.96[CEU][hapmap]
rs4348979	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs4421818	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs4768951	0.92[CEU][hapmap]
rs6580736	0.92[CEU][hapmap]
rs6580738	0.92[CEU][hapmap]
rs7132551	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7134595	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7138420	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7138622	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138945	0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs7294618	0.88[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7296291	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7307230	0.88[ASW][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7308474	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs7311973	0.95[CEU][hapmap]
rs7312252	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7486747	0.96[CEU][hapmap]
rs7953953	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs7961065	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7961112	0.88[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7972465	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7979830	0.96[CEU][hapmap]
rs9364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7315690	ATF1	cis	Artery Tibial	GTEx
rs7315690	SLC38A1	cis	parietal	SCAN
rs7315690	CELA1	cis	parietal	SCAN
rs7315690	LASS5	cis	parietal	SCAN
rs7315690	LASS5	cis	cerebellum	SCAN
rs7315690	DIP2B	cis	cerebellum	SCAN
rs7315690	CERS5	cis	Nerve Tibial	GTEx
rs7315690	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs7315690	KIAA1463	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50561800-50582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:50561800-50582600	Weak transcription	Stomach Mucosa	stomach
3	chr12:50562000-50584800	Weak transcription	K562	blood
4	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:50568600-50582000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:50570400-50592800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:50570600-50582800	Weak transcription	Small Intestine	intestine
11	chr12:50570800-50589800	Strong transcription	Fetal Stomach	stomach
12	chr12:50571800-50586000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:50571800-50586200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
16	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:50572000-50581600	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:50572000-50586000	Weak transcription	Left Ventricle	heart
20	chr12:50572200-50582200	Weak transcription	Lung	lung
21	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
22	chr12:50572600-50586200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:50575600-50586000	Weak transcription	Dnd41	blood
24	chr12:50575800-50581600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:50575800-50582400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:50575800-50582800	Weak transcription	Hela-S3	cervix
27	chr12:50575800-50585000	Weak transcription	Liver	Liver
28	chr12:50575800-50586000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:50576000-50582000	Weak transcription	Fetal Lung	lung
30	chr12:50576000-50582200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:50576000-50582400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:50576000-50582600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:50576000-50582600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:50576000-50584600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr12:50576000-50584600	Weak transcription	Fetal Thymus	thymus
36	chr12:50576000-50586200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:50576200-50582200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:50576200-50582200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:50576400-50582400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:50576600-50595000	Weak transcription	A549	lung
41	chr12:50576800-50581600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:50577200-50582400	Weak transcription	Right Atrium	heart
43	chr12:50577800-50583400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:50578600-50586200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:50578800-50583200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr12:50578800-50583400	Genic enhancers	Adipose Nuclei	Adipose
47	chr12:50578800-50583400	Genic enhancers	HMEC	breast
48	chr12:50578800-50585200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:50579000-50582200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:50579000-50582800	Enhancers	Fetal Brain Male	brain

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