Variant report

Variant	rs2938671
Chromosome Location	chr15:78732754-78732755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78722992..78724695-chr15:78731841..78733511,2	K562	blood:
2	chr15:78587653..78594388-chr15:78727556..78733158,9	MCF-7	breast:
3	chr15:78731552..78733950-chr15:78743733..78745911,2	MCF-7	breast:
4	chr15:78731227..78733467-chr3:64216080..64218992,2	MCF-7	breast:
5	chr15:78732279..78734656-chr15:78753816..78756332,3	MCF-7	breast:
6	chr15:78732336..78734017-chr15:78769375..78771802,2	K562	blood:
7	chr15:78728558..78732848-chr15:78754139..78757790,4	K562	blood:

Variant related genes	Relation type
ENSG00000140395	Chromatin interaction
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10851906	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072763	0.85[EUR][1000 genomes]
rs11072766	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12101809	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16969894	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2036529	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2036533	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568483	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2568485	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2568488	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568490	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568493	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568497	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2568498	0.89[JPT][hapmap]
rs2568499	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2656055	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2656056	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2656069	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656070	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2656071	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656072	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2656073	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656074	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28480606	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28511883	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28602670	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2869032	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2869045	0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2915695	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2938674	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2958719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35031105	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4887053	0.88[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5019044	0.94[CEU][hapmap];0.88[YRI][hapmap]
rs7174190	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7174348	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs924840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs958025	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9672608	0.84[AMR][1000 genomes];0.84[EUR][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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2938671	IREB2	cis	lesional skin	skin_eQTL
rs2938671	IREB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78731400-78734200	Weak transcription	Gastric	stomach
2	chr15:78731400-78734400	Weak transcription	Spleen	Spleen
3	chr15:78731400-78745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:78731600-78732800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:78731600-78732800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:78731600-78732800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:78731600-78732800	Weak transcription	Lung	lung
8	chr15:78731600-78732800	Weak transcription	Pancreas	Pancrea
9	chr15:78731600-78733000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:78731600-78733000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:78731600-78733000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:78731600-78734400	Weak transcription	Ovary	ovary
13	chr15:78731600-78734400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:78731600-78736800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:78731600-78740600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:78731600-78742800	Weak transcription	Esophagus	oesophagus
17	chr15:78731600-78742800	Weak transcription	Right Ventricle	heart
18	chr15:78731600-78756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
20	chr15:78731800-78733000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr15:78731800-78733000	Weak transcription	Fetal Brain Male	brain
22	chr15:78731800-78733400	Enhancers	Fetal Heart	heart
23	chr15:78731800-78733600	Enhancers	Colon Smooth Muscle	Colon
24	chr15:78731800-78738200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:78731800-78738200	Weak transcription	Colonic Mucosa	Colon
26	chr15:78731800-78740400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:78731800-78740800	Weak transcription	Stomach Mucosa	stomach
28	chr15:78732000-78732800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr15:78732000-78732800	Enhancers	Adipose Nuclei	Adipose
30	chr15:78732000-78732800	Enhancers	Fetal Brain Female	brain
31	chr15:78732000-78733000	Weak transcription	Psoas Muscle	Psoas
32	chr15:78732000-78733000	Weak transcription	Right Atrium	heart
33	chr15:78732000-78733200	Genic enhancers	Fetal Thymus	thymus
34	chr15:78732000-78733800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr15:78732000-78733800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
36	chr15:78732000-78734000	Genic enhancers	Liver	Liver
37	chr15:78732000-78734200	Weak transcription	Small Intestine	intestine
38	chr15:78732000-78735000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr15:78732000-78735200	Genic enhancers	Fetal Lung	lung
40	chr15:78732000-78736000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:78732200-78732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:78732200-78732800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:78732200-78732800	Weak transcription	Brain Anterior Caudate	brain
44	chr15:78732200-78733000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:78732200-78733000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:78732200-78733000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:78732200-78733000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr15:78732200-78733000	Genic enhancers	Hela-S3	cervix
49	chr15:78732200-78733000	Strong transcription	HSMM	muscle
50	chr15:78732200-78733200	Genic enhancers	Primary T cells fromperipheralblood	blood

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