Variant report

Variant	rs12439377
Chromosome Location	chr15:42861362-42861363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42860282-42863171	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42854171..42864590-chr15:42864872..42869799,12	K562	blood:

Variant related genes	Relation type
ENSG00000260490	TF binding region
ENSG00000159433	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10454692	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1048571	1.00[ASW][hapmap];1.00[CEU][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070375	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630625	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11630681	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11633112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11635041	0.87[EUR][1000 genomes]
rs11635076	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11635889	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11636209	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11636577	0.80[TSI][hapmap]
rs12438021	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440118	0.94[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs12440506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12910538	0.82[CEU][hapmap]
rs16973265	0.82[CEU][hapmap]
rs17708630	0.81[CEU][hapmap]
rs17709596	0.83[EUR][1000 genomes]
rs17709867	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17765354	0.82[CEU][hapmap]
rs17766258	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17767264	0.82[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17767270	0.82[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs3742999	0.82[CEU][hapmap]
rs41315252	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56069741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56172155	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62019280	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019282	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019287	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019294	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019312	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62019320	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62019322	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62022316	0.83[EUR][1000 genomes]
rs62022318	0.84[EUR][1000 genomes]
rs7182376	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72711767	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039240	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8042618	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12439377	TUBGCP4	cis	cerebellum	SCAN
rs12439377	SNAP23	cis	parietal	SCAN
rs12439377	INO80	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42841600-42866800	Weak transcription	Stomach Mucosa	stomach
2	chr15:42841800-42867000	Weak transcription	Ovary	ovary
3	chr15:42842200-42867000	Weak transcription	Psoas Muscle	Psoas
4	chr15:42842400-42867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:42842600-42867400	Weak transcription	Small Intestine	intestine
6	chr15:42842800-42867000	Weak transcription	Fetal Kidney	kidney
7	chr15:42843000-42863000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42848000-42861400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:42849200-42861400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:42849400-42866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42849800-42862800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:42850000-42861400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr15:42850000-42862800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr15:42850800-42861400	Strong transcription	Adipose Nuclei	Adipose
15	chr15:42851000-42861400	Strong transcription	Liver	Liver
16	chr15:42851000-42861800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:42851400-42862800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:42851600-42866600	Weak transcription	Fetal Heart	heart
19	chr15:42852000-42867000	Weak transcription	Colonic Mucosa	Colon
20	chr15:42853400-42861800	Strong transcription	Fetal Brain Female	brain
21	chr15:42854200-42867000	Weak transcription	HSMMtube	muscle
22	chr15:42854800-42867000	Weak transcription	Pancreas	Pancrea
23	chr15:42855000-42864400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:42855200-42867000	Weak transcription	Esophagus	oesophagus
25	chr15:42855200-42867800	Weak transcription	Aorta	Aorta
26	chr15:42856000-42867000	Weak transcription	A549	lung
27	chr15:42857600-42867000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:42857800-42867200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:42857800-42867200	Weak transcription	Spleen	Spleen
30	chr15:42858000-42867000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:42858200-42867000	Weak transcription	Right Ventricle	heart
32	chr15:42858400-42866400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:42858800-42867000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:42858800-42867000	Weak transcription	Brain Substantia Nigra	brain
35	chr15:42858800-42867000	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:42859000-42867200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:42859000-42868000	Weak transcription	Fetal Brain Male	brain
38	chr15:42859200-42866400	Weak transcription	HepG2	liver
39	chr15:42859200-42867000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr15:42859200-42867000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:42859200-42867000	Weak transcription	Brain Angular Gyrus	brain
42	chr15:42859200-42867000	Weak transcription	Fetal Lung	lung
43	chr15:42859200-42867000	Weak transcription	HSMM	muscle
44	chr15:42859200-42867000	Weak transcription	NH-A	brain
45	chr15:42859200-42867000	Weak transcription	NHEK	skin
46	chr15:42859400-42866800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:42859400-42866800	Weak transcription	Hela-S3	cervix
48	chr15:42859400-42867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:42859400-42867000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:42859400-42867000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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