Variant report

Variant	rs4942899
Chromosome Location	chr13:50507944-50507945
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	chr13:50494914..50497363-chr13:50507125..50509301,2	MCF-7	breast:
2	chr13:50507293..50510312-chr13:50568081..50571220,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11617754	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs2066549	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2066557	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs2066558	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2066572	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2066575	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2066585	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2066594	0.81[AMR][1000 genomes]
rs2242482	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2475837	0.80[ASN][1000 genomes]
rs2687951	0.81[AMR][1000 genomes]
rs2740508	0.81[AMR][1000 genomes]
rs2740524	1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2740544	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2740545	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2760914	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2803839	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2812222	0.81[AMR][1000 genomes]
rs2997624	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4548769	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4942901	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7336058	0.93[ASN][1000 genomes]
rs7338055	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73489861	0.82[ASN][1000 genomes]
rs73489862	0.82[ASN][1000 genomes]
rs790943	0.86[CHB][hapmap]
rs7986337	0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs9535407	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9568354	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9568357	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs9568363	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568364	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568366	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs9596215	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9596219	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9596220	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[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	esv1851738	chr13:50474326-50507944	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv976235	chr13:50501048-50509556	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4942899	KCNRG	cis	cerebellum	SCAN
rs4942899	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs4942899	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs4942899	PHF11	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50479600-50508600	Weak transcription	K562	blood
2	chr13:50480800-50508800	Weak transcription	Fetal Brain Male	brain
3	chr13:50481800-50509600	Weak transcription	Right Ventricle	heart
4	chr13:50482600-50509600	Weak transcription	Primary B cells from cord blood	blood
5	chr13:50484000-50509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:50484400-50509400	Weak transcription	Fetal Kidney	kidney
7	chr13:50484600-50509600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:50485800-50509200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr13:50486000-50509400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:50486400-50509600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr13:50486600-50508800	Weak transcription	Hela-S3	cervix
12	chr13:50487400-50509400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr13:50487600-50509400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:50488400-50509600	Weak transcription	Colonic Mucosa	Colon
15	chr13:50489200-50509600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:50489200-50510000	Weak transcription	Spleen	Spleen
17	chr13:50492200-50509400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr13:50492400-50509600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr13:50492600-50508800	Weak transcription	HUVEC	blood vessel
20	chr13:50492800-50509400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr13:50492800-50509600	Weak transcription	Aorta	Aorta
22	chr13:50493400-50509400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr13:50493800-50509600	Weak transcription	Lung	lung
24	chr13:50494200-50508800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:50494400-50508800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr13:50495400-50509600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr13:50495800-50508400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:50495800-50508800	Weak transcription	Brain Substantia Nigra	brain
29	chr13:50495800-50508800	Weak transcription	Fetal Brain Female	brain
30	chr13:50495800-50508800	Weak transcription	HepG2	liver
31	chr13:50497400-50509400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr13:50499000-50508800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr13:50499000-50509400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:50499600-50509600	Weak transcription	Esophagus	oesophagus
35	chr13:50500000-50509400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:50500000-50509800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr13:50500400-50508800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr13:50500400-50508800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr13:50500400-50508800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr13:50500400-50508800	Weak transcription	Brain Hippocampus Middle	brain
41	chr13:50500600-50509200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr13:50500800-50508800	Weak transcription	GM12878-XiMat	blood
43	chr13:50501200-50508800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:50502000-50508200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr13:50502000-50508800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:50502000-50509400	Weak transcription	HSMMtube	muscle
47	chr13:50502200-50509400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr13:50502400-50508800	Weak transcription	Brain Anterior Caudate	brain
49	chr13:50502600-50509600	Weak transcription	Pancreas	Pancrea
50	chr13:50502600-50509800	Weak transcription	Gastric	stomach

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