Variant report

Variant	rs228804
Chromosome Location	chr6:39071810-39071811
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	chr6:39071474..39074131-chr6:39080947..39082685,2	MCF-7	breast:
2	chr6:39071727..39073365-chr6:39081349..39083431,2	K562	blood:

Variant related genes	Relation type
ENSG00000112167	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2143733	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2746304	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380828	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470967	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761050	chr6:39066867-39072034	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3472497	chr6:39068376-39073004	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3472498	chr6:39068422-39072935	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3472499	chr6:39068422-39072935	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv514357	chr6:39068898-39072054	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv441994	chr6:39068912-39072032	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2422109	chr6:39068912-39072681	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv12858	chr6:39068929-39072849	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv516974	chr6:39069268-39072034	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv3692894	chr6:39069268-39072681	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs228804	SAYSD1	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39021200-39072000	Weak transcription	Gastric	stomach
2	chr6:39027400-39073000	Weak transcription	Pancreas	Pancrea
3	chr6:39043400-39082000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:39053000-39072400	Weak transcription	Brain Germinal Matrix	brain
5	chr6:39058400-39072000	Weak transcription	Left Ventricle	heart
6	chr6:39058400-39072600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:39058400-39073000	Weak transcription	Lung	lung
8	chr6:39060400-39073200	Weak transcription	Fetal Heart	heart
9	chr6:39060600-39072800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:39062000-39072000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:39062600-39072200	Weak transcription	Small Intestine	intestine
12	chr6:39063800-39072200	Weak transcription	Liver	Liver
13	chr6:39063800-39076400	Weak transcription	HepG2	liver
14	chr6:39064800-39076800	Weak transcription	Aorta	Aorta
15	chr6:39065000-39072400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:39066400-39072000	Weak transcription	Right Ventricle	heart
17	chr6:39066800-39077200	Weak transcription	Brain Anterior Caudate	brain
18	chr6:39067600-39073000	Enhancers	Fetal Lung	lung
19	chr6:39068200-39082000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:39068400-39075600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:39068600-39072200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:39068600-39072400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:39068600-39073000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:39068600-39073000	Weak transcription	Colonic Mucosa	Colon
25	chr6:39068600-39077200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:39068600-39078400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:39068800-39077800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:39068800-39078200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:39069000-39072800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:39069200-39072400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:39069200-39072600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:39069200-39076800	Weak transcription	Spleen	Spleen
33	chr6:39069400-39072000	Weak transcription	Adipose Nuclei	Adipose
34	chr6:39069400-39072400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:39069400-39076800	Weak transcription	HSMMtube	muscle
36	chr6:39069400-39077600	Weak transcription	HMEC	breast
37	chr6:39069600-39072000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:39069600-39073000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:39069800-39072200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:39069800-39072400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:39069800-39073800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:39069800-39081800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr6:39070000-39072000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:39070000-39072000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:39070000-39077200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:39070200-39072000	Weak transcription	Fetal Intestine Small	intestine
47	chr6:39070200-39072800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:39070200-39073600	Strong transcription	Thymus	Thymus
49	chr6:39070200-39073800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr6:39070200-39076400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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