Variant report

Variant	rs41530251
Chromosome Location	chr19:41316355-41316356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41222253..41224407-chr19:41315424..41318276,2	K562	blood:
2	chr19:41221543..41224231-chr19:41314588..41316621,2	MCF-7	breast:
3	chr19:41221999..41223753-chr19:41315424..41317151,2	K562	blood:
4	chr19:41280805..41286068-chr19:41308324..41316733,13	K562	blood:
5	chr19:41220720..41224635-chr19:41312175..41316788,5	MCF-7	breast:
6	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:

Variant related genes	Relation type
ENSG00000188493	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11547373	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12052092	0.85[ASN][1000 genomes]
rs12151282	0.85[JPT][hapmap]
rs2305797	0.85[MKK][hapmap]
rs35061187	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35405967	0.81[ASN][1000 genomes]
rs3733829	0.84[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3736329	0.84[ASW][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3776611	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4802090	0.86[ASN][1000 genomes]
rs4802091	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4803369	0.84[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.80[TSI][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7245595	0.81[JPT][hapmap]
rs73048928	0.82[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	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv521459	chr19:41313202-41333284	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41530251	EHD2	cis	cerebellum	SCAN
rs41530251	OR6C1	trans	cerebellum	SCAN
rs41530251	KCNN4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41306400-41316800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:41308400-41316400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:41309800-41316400	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr19:41311200-41316400	Strong transcription	Dnd41	blood
5	chr19:41313000-41316400	Weak transcription	Fetal Kidney	kidney
6	chr19:41313400-41316400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr19:41313400-41316400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
8	chr19:41313600-41316600	Weak transcription	Fetal Brain Male	brain
9	chr19:41314600-41316600	Weak transcription	Hela-S3	cervix
10	chr19:41314800-41316600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:41315000-41316600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr19:41315000-41324400	Weak transcription	HepG2	liver
13	chr19:41315000-41332600	Weak transcription	Aorta	Aorta
14	chr19:41315400-41316400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:41315400-41316400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:41315400-41316400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
17	chr19:41315400-41316400	Genic enhancers	HMEC	breast
18	chr19:41315400-41316600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:41315400-41317400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:41315600-41316400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:41315600-41316400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr19:41315600-41316600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr19:41315600-41316600	Weak transcription	Fetal Brain Female	brain
24	chr19:41315600-41316800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr19:41315800-41316400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:41315800-41316400	Enhancers	Placenta Amnion	Placenta Amnion
27	chr19:41315800-41316400	Enhancers	Psoas Muscle	Psoas
28	chr19:41315800-41316400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr19:41315800-41316600	Enhancers	Primary hematopoietic stem cells	blood
30	chr19:41315800-41316600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr19:41315800-41316600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:41315800-41316600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:41315800-41316600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr19:41315800-41316600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:41315800-41316600	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr19:41315800-41316600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:41315800-41316600	Weak transcription	Ovary	ovary
38	chr19:41315800-41316800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:41315800-41317000	Enhancers	Liver	Liver
40	chr19:41315800-41318000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr19:41315800-41318400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:41316000-41316400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr19:41316000-41316400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:41316000-41316400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:41316000-41316400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr19:41316000-41316400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr19:41316000-41316400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr19:41316000-41316400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:41316000-41316400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr19:41316000-41316400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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