Variant report

Variant	rs9972424
Chromosome Location	chr15:40365851-40365852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40361459..40366979-chr15:40389781..40395512,5	MCF-7	breast:
2	chr15:40355457..40358717-chr15:40360057..40366974,8	K562	blood:

Variant related genes	Relation type
ENSG00000248508	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11638521	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12440899	0.89[JPT][hapmap]
rs12441483	0.89[JPT][hapmap]
rs16970286	0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16970291	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16970319	0.87[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs17723133	0.87[CEU][hapmap]
rs28361302	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28371998	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28379715	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28477230	0.83[ASN][1000 genomes]
rs28479712	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28534747	0.89[EUR][1000 genomes]
rs28537079	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28587891	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605815	0.91[ASN][1000 genomes]
rs28620926	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3923235	0.87[CEU][hapmap]
rs4923850	0.89[JPT][hapmap]
rs4923852	0.83[EUR][1000 genomes]
rs4924410	0.87[CEU][hapmap]
rs4924412	0.89[JPT][hapmap]
rs4924413	0.87[CEU][hapmap]
rs4924415	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924416	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181230	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7183977	0.95[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs7497289	0.80[CEU][hapmap]
rs749749	0.89[JPT][hapmap]
rs8026641	0.87[CEU][hapmap]
rs9972442	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9972424	SRP14	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40346000-40367400	Weak transcription	K562	blood
2	chr15:40346200-40372800	Weak transcription	Fetal Kidney	kidney
3	chr15:40359000-40368000	Weak transcription	Ovary	ovary
4	chr15:40359800-40366000	Enhancers	Fetal Thymus	thymus
5	chr15:40361800-40368400	Weak transcription	HMEC	breast
6	chr15:40362200-40367600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:40362200-40367600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:40362200-40368800	Weak transcription	Osteobl	bone
9	chr15:40362200-40372600	Weak transcription	Small Intestine	intestine
10	chr15:40362200-40373000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:40362200-40373600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:40362400-40367400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:40362400-40367600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:40362400-40368000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:40362400-40369200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:40362400-40372800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:40362400-40374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:40362600-40367200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:40362600-40367600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:40362600-40367600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:40362600-40367600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:40362600-40367600	Weak transcription	Spleen	Spleen
23	chr15:40362600-40367600	Weak transcription	A549	lung
24	chr15:40362600-40370800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:40362600-40373800	Weak transcription	Aorta	Aorta
26	chr15:40362800-40367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:40362800-40367600	Weak transcription	Hela-S3	cervix
28	chr15:40362800-40372400	Weak transcription	GM12878-XiMat	blood
29	chr15:40363000-40367400	Weak transcription	HepG2	liver
30	chr15:40364600-40366200	Flanking Active TSS	Thymus	Thymus
31	chr15:40364600-40373000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:40364800-40366000	Weak transcription	Pancreas	Pancrea
33	chr15:40364800-40376800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:40365000-40366800	Weak transcription	Stomach Mucosa	stomach
35	chr15:40365000-40367400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr15:40365000-40367400	Weak transcription	Lung	lung
37	chr15:40365000-40367600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:40365000-40368800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr15:40365000-40373200	Weak transcription	Left Ventricle	heart
40	chr15:40365200-40367400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:40365200-40367400	Weak transcription	HUVEC	blood vessel
42	chr15:40365200-40368000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr15:40365200-40368800	Weak transcription	Placenta	Placenta
44	chr15:40365400-40366200	Enhancers	Primary hematopoietic stem cells	blood
45	chr15:40365400-40367000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:40365400-40367600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:40365600-40367400	Weak transcription	Gastric	stomach
48	chr15:40365600-40369000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:40365600-40372400	Weak transcription	Fetal Heart	heart
50	chr15:40365600-40374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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