Variant report

Variant	rs568901
Chromosome Location	chr6:33710038-33710039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33706241..33709561-chr6:33709640..33714031,4	MCF-7	breast:
2	chr6:33708694..33710403-chr6:33728367..33730684,2	MCF-7	breast:
3	chr6:33708535..33711845-chr6:33715070..33719242,6	MCF-7	breast:
4	chr6:33704170..33706170-chr6:33708932..33711756,3	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2182658	0.82[JPT][hapmap]
rs482786	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs545787	0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs756138	0.82[JPT][hapmap]
rs756139	0.82[JPT][hapmap]
rs7739273	0.82[JPT][hapmap]
rs7752348	0.82[JPT][hapmap]
rs9380379	0.82[JPT][hapmap]
rs943465	0.82[JPT][hapmap]
rs943476	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs568901	SRPK1	cis	parietal	SCAN
rs568901	LEMD2	cis	cerebellum	SCAN
rs568901	MTCH1	cis	parietal	SCAN
rs568901	C6orf129	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:33705400-33712000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:33705800-33711000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:33706600-33715800	Enhancers	Fetal Intestine Large	intestine
10	chr6:33706800-33711400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:33707000-33710200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:33707200-33711400	Enhancers	Fetal Brain Male	brain
13	chr6:33707400-33714000	Weak transcription	Spleen	Spleen
14	chr6:33707600-33711000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:33707800-33710200	Enhancers	Brain Substantia Nigra	brain
16	chr6:33707800-33710600	Genic enhancers	Muscle Satellite Cultured Cells	--
17	chr6:33708000-33710200	Weak transcription	Psoas Muscle	Psoas
18	chr6:33708200-33710400	Enhancers	Stomach Mucosa	stomach
19	chr6:33708600-33710800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:33708600-33711600	Weak transcription	HMEC	breast
21	chr6:33708800-33710400	Weak transcription	Fetal Lung	lung
22	chr6:33709000-33710600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:33709000-33710600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:33709000-33711400	Weak transcription	Liver	Liver
25	chr6:33709000-33711600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:33709000-33711600	Weak transcription	HepG2	liver
27	chr6:33709000-33711800	Weak transcription	Hela-S3	cervix
28	chr6:33709000-33712000	Weak transcription	Gastric	stomach
29	chr6:33709000-33712400	Weak transcription	Fetal Heart	heart
30	chr6:33709200-33710200	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:33709200-33710200	Weak transcription	Lung	lung
32	chr6:33709200-33710400	Weak transcription	Fetal Brain Female	brain
33	chr6:33709200-33710600	Weak transcription	Brain Angular Gyrus	brain
34	chr6:33709200-33710600	Weak transcription	Brain Anterior Caudate	brain
35	chr6:33709200-33710800	Weak transcription	Pancreas	Pancrea
36	chr6:33709200-33711800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:33709400-33710400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:33709800-33710200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:33709800-33710200	Enhancers	Fetal Intestine Small	intestine
40	chr6:33709800-33710200	Genic enhancers	Right Atrium	heart
41	chr6:33709800-33710800	Enhancers	HSMMtube	muscle
42	chr6:33709800-33711000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:33709800-33711200	Enhancers	Placenta	Placenta
44	chr6:33710000-33710400	Strong transcription	Brain Cingulate Gyrus	brain
45	chr6:33710000-33710400	Genic enhancers	Brain Hippocampus Middle	brain
46	chr6:33710000-33710600	Genic enhancers	Left Ventricle	heart
47	chr6:33710000-33711000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:33710000-33711000	Transcr. at gene 5' and 3'	Right Ventricle	heart
49	chr6:33710000-33711200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:33710000-33711200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle

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