Variant report

Variant	rs3798657
Chromosome Location	chr6:119667666-119667667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119648699..119654492-chr6:119662714..119668241,6	K562	blood:
2	chr6:119606943..119609052-chr6:119667352..119668942,2	K562	blood:
3	chr6:119649666..119652399-chr6:119665160..119668137,2	K562	blood:
4	chr6:119666514..119668057-chr6:120002574..120005085,2	MCF-7	breast:
5	chr6:119666964..119669354-chr6:119827597..119829582,2	K562	blood:
6	chr6:119658599..119660724-chr6:119666324..119670101,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17052758	0.81[AMR][1000 genomes]
rs17080943	0.81[AMR][1000 genomes]
rs17081398	0.81[CEU][hapmap]
rs17588322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17588655	0.81[AMR][1000 genomes]
rs1935477	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs3778107	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes]
rs56969807	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57719766	0.81[AMR][1000 genomes]
rs72952938	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72962556	0.81[AMR][1000 genomes]
rs72964499	0.81[AMR][1000 genomes]
rs72968477	0.81[AMR][1000 genomes]
rs72970359	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798657	BRD7P3	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119625200-119668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:119636200-119667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:119641400-119668200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:119645000-119668200	Weak transcription	Aorta	Aorta
5	chr6:119648200-119668000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:119648200-119668000	Weak transcription	Esophagus	oesophagus
7	chr6:119653200-119667800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:119658800-119667800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:119661200-119668000	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:119661400-119668000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:119661600-119667800	Weak transcription	Primary T cells from cord blood	blood
12	chr6:119661600-119667800	Transcr. at gene 5' and 3'	HepG2	liver
13	chr6:119662200-119669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:119662600-119668600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:119662800-119667800	Weak transcription	Fetal Thymus	thymus
16	chr6:119664000-119668200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:119664400-119668600	Transcr. at gene 5' and 3'	K562	blood
18	chr6:119664800-119672400	Active TSS	Brain Anterior Caudate	brain
19	chr6:119665000-119668600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr6:119665000-119669200	Weak transcription	Spleen	Spleen
21	chr6:119665200-119667800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:119665200-119672800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:119665600-119667800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:119665600-119668600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr6:119665800-119668000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
26	chr6:119665800-119668200	Weak transcription	Ovary	ovary
27	chr6:119666200-119672600	Active TSS	NHDF-Ad	bronchial
28	chr6:119666600-119668200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:119666600-119668600	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr6:119666600-119672400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:119666800-119668200	Active TSS	Stomach Smooth Muscle	stomach
32	chr6:119666800-119669000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:119666800-119669000	Flanking Active TSS	GM12878-XiMat	blood
34	chr6:119667000-119667800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr6:119667000-119667800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr6:119667000-119668000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:119667000-119668200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:119667000-119669400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:119667000-119672400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:119667000-119672400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:119667000-119672800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:119667200-119667800	Active TSS	Psoas Muscle	Psoas
43	chr6:119667200-119668000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:119667200-119668000	Active TSS	Colon Smooth Muscle	Colon
45	chr6:119667200-119668200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:119667200-119668200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:119667200-119668200	Enhancers	Small Intestine	intestine
48	chr6:119667200-119668400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:119667200-119669200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr6:119667200-119672200	Active TSS	Brain Inferior Temporal Lobe	brain

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