Variant report

Variant	rs2398
Chromosome Location	chr15:52407409-52407410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52263208..52265625-chr15:52404085..52407650,4	MCF-7	breast:
2	chr15:52404951..52408390-chr15:52415652..52417848,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BCL2L10-1	chr15:52407274-52408261	XLOC_011480

Variant related genes	Relation type
ENSG00000166477	Chromatin interaction
ENSG00000259709	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070882	0.85[ASN][1000 genomes]
rs11855672	0.80[MEX][hapmap]
rs11856177	0.85[ASN][1000 genomes]
rs12438194	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12438743	0.82[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12438937	0.93[GIH][hapmap];0.80[AMR][1000 genomes]
rs12440956	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593041	0.93[GIH][hapmap];0.80[AMR][1000 genomes]
rs12594679	0.83[ASN][1000 genomes]
rs12595160	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs12899030	0.86[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.81[ASN][1000 genomes]
rs12899343	0.86[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.81[ASN][1000 genomes]
rs12901354	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901730	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12901891	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12902073	1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12903769	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12904831	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12904889	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12907835	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12908742	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12908833	0.84[ASN][1000 genomes]
rs12909161	0.82[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12909184	0.89[GIH][hapmap];1.00[YRI][hapmap]
rs12909880	0.82[AMR][1000 genomes]
rs12910398	1.00[YRI][hapmap]
rs12912428	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916557	0.85[ASN][1000 genomes]
rs2227308	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2231297	1.00[CEU][hapmap];0.83[GIH][hapmap];0.84[EUR][1000 genomes]
rs2414130	1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[EUR][1000 genomes]
rs2414132	0.93[CEU][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34283892	0.83[ASN][1000 genomes]
rs35827106	0.85[ASN][1000 genomes]
rs3794540	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3794543	0.92[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4636859	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4638520	0.86[CHB][hapmap];0.93[GIH][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4774608	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4776003	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4776010	0.80[MEX][hapmap]
rs62014721	0.83[AMR][1000 genomes]
rs62014722	0.83[AMR][1000 genomes]
rs7164508	1.00[YRI][hapmap]
rs7177248	0.82[CHB][hapmap]
rs8034097	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2398	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs2398	FGF7	cis	cerebellum	SCAN
rs2398	ARPP19	cis	parietal	SCAN
rs2398	KIAA1370	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52404800-52407600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:52404800-52407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:52404800-52408000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:52404800-52408200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:52404800-52408400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:52404800-52409800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:52404800-52410600	Enhancers	Adipose Nuclei	Adipose
9	chr15:52404800-52416400	Weak transcription	Aorta	Aorta
10	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:52405000-52407600	Weak transcription	HUVEC	blood vessel
12	chr15:52405000-52407800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:52405000-52407800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:52405000-52408000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:52405000-52408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:52405000-52408400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:52405000-52409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:52405000-52411800	Weak transcription	Ovary	ovary
19	chr15:52405000-52412000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:52405000-52413200	Weak transcription	Primary T cells from cord blood	blood
21	chr15:52405000-52414800	Weak transcription	Primary B cells from cord blood	blood
22	chr15:52405000-52416400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:52405000-52416400	Weak transcription	Gastric	stomach
24	chr15:52405000-52416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:52405000-52416600	Weak transcription	Esophagus	oesophagus
26	chr15:52405000-52420400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:52405000-52421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:52405000-52427400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
31	chr15:52405200-52407600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:52405200-52407800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:52405200-52408200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:52405200-52412400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:52405400-52426000	Weak transcription	Spleen	Spleen
36	chr15:52405600-52408000	Enhancers	HepG2	liver
37	chr15:52405600-52412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:52405800-52407800	Enhancers	Fetal Muscle Leg	muscle
39	chr15:52405800-52408000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:52405800-52408000	Weak transcription	GM12878-XiMat	blood
41	chr15:52406000-52408000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr15:52406000-52410200	Enhancers	Brain Germinal Matrix	brain
43	chr15:52406000-52412400	Weak transcription	Thymus	Thymus
44	chr15:52406000-52414200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:52406200-52407800	Enhancers	Brain Hippocampus Middle	brain
46	chr15:52406200-52407800	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr15:52406400-52407600	Weak transcription	Fetal Intestine Small	intestine
48	chr15:52406400-52408000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:52406400-52408000	Enhancers	Brain Cingulate Gyrus	brain
50	chr15:52406400-52408400	Enhancers	Cortex derived primary cultured neurospheres	brain

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