Variant report

Variant	rs6923822
Chromosome Location	chr6:128839470-128839471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:128582093..128584697-chr6:128837885..128840735,2	MCF-7	breast:
2	chr6:128401254..128402898-chr6:128838085..128840058,2	MCF-7	breast:
3	chr6:128810906..128814817-chr6:128838628..128842024,3	MCF-7	breast:
4	chr6:128838418..128841487-chr6:128915011..128917718,3	MCF-7	breast:
5	chr6:128598470..128600441-chr6:128838939..128840470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10085247	0.87[EUR][1000 genomes]
rs10085248	0.87[EUR][1000 genomes]
rs10223535	0.83[EUR][1000 genomes]
rs10872331	0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11154439	0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11963575	0.84[EUR][1000 genomes]
rs12526667	0.94[CEU][hapmap]
rs13437323	0.94[CEU][hapmap]
rs1361595	0.83[EUR][1000 genomes]
rs1417895	1.00[CHB][hapmap]
rs1417896	1.00[CHB][hapmap]
rs17053280	1.00[CHD][hapmap]
rs17055938	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17055952	0.87[EUR][1000 genomes]
rs2326702	0.89[CEU][hapmap]
rs60719752	0.87[AFR][1000 genomes]
rs62426794	0.88[EUR][1000 genomes]
rs62426845	1.00[ASN][1000 genomes]
rs6569533	0.81[EUR][1000 genomes]
rs6569535	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6569536	1.00[CHB][hapmap]
rs6920943	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6924111	0.85[EUR][1000 genomes]
rs6935611	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs717617	0.82[CEU][hapmap]
rs7356823	1.00[CHB][hapmap]
rs7356912	0.87[EUR][1000 genomes]
rs7745291	0.81[EUR][1000 genomes]
rs7751265	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7752487	0.94[CEU][hapmap]
rs7765212	0.95[CEU][hapmap]
rs7771701	0.80[CEU][hapmap]
rs9321121	1.00[CHB][hapmap]
rs9375570	1.00[CHB][hapmap]
rs9375572	1.00[CHB][hapmap]
rs9375575	0.81[EUR][1000 genomes]
rs9385464	1.00[CHB][hapmap]
rs9388638	1.00[CHB][hapmap]
rs9388645	1.00[CHB][hapmap]
rs9388646	1.00[CHB][hapmap]
rs9402057	1.00[CHB][hapmap]
rs947358	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9482893	0.83[EUR][1000 genomes]
rs9482904	0.89[CEU][hapmap]
rs9491960	1.00[CHD][hapmap]
rs9491965	1.00[CHD][hapmap]
rs9491973	1.00[CHD][hapmap]
rs9491990	0.85[EUR][1000 genomes]
rs9491999	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs9492001	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap]
rs9492021	0.80[CEU][hapmap]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6923822	SAMD3	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
3	chr6:128825800-128840000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:128829400-128839600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:128830000-128839600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:128831400-128840000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:128831600-128839800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:128832600-128839600	Weak transcription	Gastric	stomach
9	chr6:128832800-128839600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:128832800-128839800	Weak transcription	Right Ventricle	heart
11	chr6:128835000-128840600	Active TSS	Fetal Brain Female	brain
12	chr6:128835800-128839600	Enhancers	Fetal Lung	lung
13	chr6:128835800-128839800	Weak transcription	Small Intestine	intestine
14	chr6:128836400-128839600	Enhancers	Rectal Smooth Muscle	rectum
15	chr6:128837000-128840000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:128837200-128839800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:128837200-128842800	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr6:128837400-128839600	Weak transcription	Placenta	Placenta
19	chr6:128837400-128839600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:128837600-128839600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr6:128837600-128839600	Enhancers	Fetal Kidney	kidney
22	chr6:128837600-128839800	Weak transcription	Psoas Muscle	Psoas
23	chr6:128837600-128840000	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:128837800-128839600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:128837800-128839600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:128838000-128839600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:128838000-128839600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:128838000-128839600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:128838000-128839800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:128838200-128839600	Flanking Active TSS	NHLF	lung
31	chr6:128838200-128842400	Active TSS	Brain Cingulate Gyrus	brain
32	chr6:128838400-128839600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:128838400-128839600	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:128838400-128839600	Weak transcription	Left Ventricle	heart
35	chr6:128838400-128839600	Weak transcription	Pancreas	Pancrea
36	chr6:128838400-128839800	Weak transcription	Lung	lung
37	chr6:128838400-128842200	Active TSS	Duodenum Mucosa	Duodenum
38	chr6:128838400-128843000	Active TSS	Fetal Brain Male	brain
39	chr6:128838600-128839600	Weak transcription	Fetal Stomach	stomach
40	chr6:128838600-128839800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:128838600-128842200	Active TSS	HMEC	breast
42	chr6:128838600-128842400	Active TSS	Fetal Intestine Small	intestine
43	chr6:128838600-128842600	Active TSS	Brain Hippocampus Middle	brain
44	chr6:128838600-128842600	Active TSS	Fetal Intestine Large	intestine
45	chr6:128838600-128842800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:128838600-128842800	Active TSS	Brain Angular Gyrus	brain
47	chr6:128838800-128839600	Weak transcription	Ovary	ovary
48	chr6:128838800-128839600	Enhancers	Hela-S3	cervix
49	chr6:128838800-128839600	Weak transcription	HSMM	muscle
50	chr6:128838800-128840400	Flanking Active TSS	HUVEC	blood vessel

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