Variant report

Variant	rs9378950
Chromosome Location	chr6:5435871-5435872
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:5435025..5437230-chr6:5438877..5440438,2	MCF-7	breast:
2	chr6:5431881..5436604-chr6:5436753..5441713,4	K562	blood:
3	chr6:5434559..5437034-chr6:5438817..5440512,2	MCF-7	breast:
4	chr6:5431424..5433341-chr6:5434266..5436505,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10900967	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12198170	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1895645	0.83[YRI][hapmap]
rs200198	0.90[CHD][hapmap]
rs200201	0.82[ASN][1000 genomes]
rs2113691	0.86[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[ASN][1000 genomes]
rs2326610	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2432762	0.86[CHD][hapmap]
rs2432793	0.83[YRI][hapmap]
rs2503813	0.87[GIH][hapmap]
rs6922067	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs6938112	0.93[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328299	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9328300	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9328301	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9328302	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9378949	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9392686	0.86[ASW][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9405268	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9405832	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9405833	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1015643	chr6:5311590-5452427	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1030744	chr6:5328012-5458222	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1022505	chr6:5388025-5449240	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv600885	chr6:5424762-5455161	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9378950	LY86	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5399200-5440000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:5403200-5439800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:5403400-5445200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:5403600-5437600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:5405400-5439800	Weak transcription	Pancreas	Pancrea
6	chr6:5407400-5439600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:5412800-5437000	Weak transcription	Ovary	ovary
8	chr6:5412800-5439400	Weak transcription	Spleen	Spleen
9	chr6:5413400-5442800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:5417000-5440400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:5420200-5436200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:5421600-5455000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:5421600-5455400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:5421600-5457400	Weak transcription	Fetal Intestine Small	intestine
15	chr6:5422800-5444000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:5423000-5436200	Weak transcription	NHLF	lung
17	chr6:5424400-5440000	Weak transcription	Small Intestine	intestine
18	chr6:5426200-5439400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:5426400-5436200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:5428200-5437800	Weak transcription	GM12878-XiMat	blood
21	chr6:5428600-5437200	Weak transcription	Dnd41	blood
22	chr6:5429000-5439400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:5429200-5443000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:5429800-5442600	Weak transcription	NHEK	skin
25	chr6:5430000-5443600	Weak transcription	Right Ventricle	heart
26	chr6:5430200-5440000	Weak transcription	Liver	Liver
27	chr6:5430400-5441800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:5430400-5443600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:5430600-5439800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:5430600-5443600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:5431400-5439400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:5431600-5439800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:5431800-5436600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:5431800-5439400	Weak transcription	HepG2	liver
35	chr6:5432000-5437800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr6:5432000-5438600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:5432000-5439200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:5432000-5439400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:5432000-5439400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:5432000-5439800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:5432200-5438600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:5432200-5438800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:5433200-5443400	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:5433400-5436800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:5433400-5443600	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:5433400-5453800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:5433600-5437600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr6:5433600-5457400	Weak transcription	Left Ventricle	heart
49	chr6:5433600-5461400	Weak transcription	Fetal Stomach	stomach
50	chr6:5433800-5436200	Weak transcription	Primary B cells from cord blood	blood

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