Variant report

Variant	rs9378919
Chromosome Location	chr6:4915841-4915842
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	chr6:4907717..4910185-chr6:4913859..4916843,2	MCF-7	breast:
2	chr6:4914506..4916957-chr6:4923942..4927545,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13197142	1.00[ASW][hapmap]
rs17284610	1.00[ASW][hapmap]
rs17356490	1.00[ASW][hapmap]
rs1891045	0.87[EUR][1000 genomes]
rs1891046	0.83[ASN][1000 genomes]
rs2179269	0.89[AMR][1000 genomes]
rs3930304	0.94[ASN][1000 genomes]
rs4144546	0.94[ASN][1000 genomes]
rs4960046	0.87[EUR][1000 genomes]
rs4960049	0.96[ASN][1000 genomes]
rs62384662	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62384663	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62384665	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62386575	0.89[AMR][1000 genomes]
rs62386578	0.89[AMR][1000 genomes]
rs62386584	0.94[AMR][1000 genomes]
rs62386585	0.94[AMR][1000 genomes]
rs62386587	0.89[AMR][1000 genomes]
rs62386590	0.89[AMR][1000 genomes]
rs62386591	0.94[AMR][1000 genomes]
rs62386593	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62386594	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62386612	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62386614	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6904931	0.97[ASN][1000 genomes]
rs6910368	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs6918626	0.85[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs6924037	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738275	0.94[ASN][1000 genomes]
rs7738459	0.94[ASN][1000 genomes]
rs7739834	0.94[ASN][1000 genomes]
rs7742807	0.81[ASN][1000 genomes]
rs7759221	0.94[ASN][1000 genomes]
rs7770206	0.94[ASN][1000 genomes]
rs7771387	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs808608	0.88[EUR][1000 genomes]
rs9378917	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9378918	0.97[ASN][1000 genomes]
rs9378920	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9392068	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9392640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392641	0.90[ASN][1000 genomes]
rs9405786	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9378919	SERPINB9	cis	cerebellum	SCAN
rs9378919	WRNIP1	cis	cerebellum	SCAN
rs9378919	FOXF2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4895000-4917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:4900200-4918800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:4902000-4918400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:4905800-4931200	Weak transcription	HepG2	liver
5	chr6:4907600-4925200	Weak transcription	Fetal Heart	heart
6	chr6:4908000-4935600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:4908200-4917000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:4908200-4934800	Weak transcription	Primary B cells from cord blood	blood
9	chr6:4908800-4920800	Weak transcription	Thymus	Thymus
10	chr6:4908800-4924400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:4909000-4916600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:4910800-4916600	Weak transcription	GM12878-XiMat	blood
13	chr6:4911000-4930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:4911000-4935200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr6:4912800-4916000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:4912800-4916600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:4912800-4931200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:4913000-4916000	Enhancers	Ovary	ovary
19	chr6:4913000-4917000	Enhancers	Psoas Muscle	Psoas
20	chr6:4913000-4918600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:4913200-4936000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:4913200-4941000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:4913400-4917000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:4913600-4916400	Enhancers	Fetal Lung	lung
25	chr6:4913600-4919200	Enhancers	Primary T cells from cord blood	blood
26	chr6:4913600-4938000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr6:4913800-4916200	Enhancers	Fetal Stomach	stomach
28	chr6:4914000-4916000	Enhancers	Fetal Kidney	kidney
29	chr6:4914000-4917200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:4914000-4918200	Enhancers	Fetal Thymus	thymus
31	chr6:4914000-4930600	Weak transcription	A549	lung
32	chr6:4914200-4916000	Enhancers	NHLF	lung
33	chr6:4914200-4916400	Enhancers	Spleen	Spleen
34	chr6:4914200-4918400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr6:4914600-4918200	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr6:4914800-4916000	Weak transcription	Right Ventricle	heart
37	chr6:4914800-4917000	Strong transcription	Fetal Intestine Small	intestine
38	chr6:4914800-4918400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:4914800-4919000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:4914800-4920200	Weak transcription	K562	blood
41	chr6:4914800-4920800	Weak transcription	Colonic Mucosa	Colon
42	chr6:4914800-4922200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:4914800-4924600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:4914800-4930400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:4914800-4930400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:4915000-4916000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:4915000-4916000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:4915000-4919200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:4915000-4919200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:4915000-4921200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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