Variant report

Variant	rs210625
Chromosome Location	chr6:117874257-117874258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:117802413..117805335-chr6:117870908..117875397,4	MCF-7	breast:
2	chr6:117873838..117876226-chr6:117922236..117924063,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047932	Chromatin interaction
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10457315	0.82[CEU][hapmap]
rs210616	0.81[ASN][1000 genomes]
rs210617	0.82[CEU][hapmap]
rs210619	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs210620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs210621	0.80[ASN][1000 genomes]
rs210627	0.81[ASN][1000 genomes]
rs210628	0.81[ASN][1000 genomes]
rs210631	0.81[ASN][1000 genomes]
rs210632	0.81[ASN][1000 genomes]
rs210634	0.81[ASN][1000 genomes]
rs210636	0.81[ASN][1000 genomes]
rs210638	0.81[ASN][1000 genomes]
rs210643	0.81[ASN][1000 genomes]
rs2134087	0.81[ASN][1000 genomes]
rs389663	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs8088	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9320608	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9320609	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489217	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs210625	TSPYL1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117869800-117880000	Weak transcription	Aorta	Aorta
2	chr6:117869800-117880000	Weak transcription	Brain Substantia Nigra	brain
3	chr6:117869800-117882600	Weak transcription	Brain Germinal Matrix	brain
4	chr6:117869800-117883200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:117869800-117884200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:117869800-117884400	Weak transcription	Ovary	ovary
7	chr6:117869800-117885200	Weak transcription	Fetal Stomach	stomach
8	chr6:117869800-117889000	Weak transcription	Left Ventricle	heart
9	chr6:117869800-117889400	Weak transcription	Psoas Muscle	Psoas
10	chr6:117869800-117889600	Weak transcription	Colonic Mucosa	Colon
11	chr6:117869800-117894400	Weak transcription	Lung	lung
12	chr6:117869800-117903800	Weak transcription	Spleen	Spleen
13	chr6:117869800-117904000	Weak transcription	Gastric	stomach
14	chr6:117869800-117904000	Weak transcription	Pancreas	Pancrea
15	chr6:117870000-117877000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:117870000-117879800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:117870000-117881600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:117870000-117881800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:117870000-117882600	Weak transcription	Adipose Nuclei	Adipose
20	chr6:117870000-117884200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:117870000-117886800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:117870200-117876600	Weak transcription	Liver	Liver
23	chr6:117870200-117879400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:117870200-117884200	Weak transcription	Fetal Brain Male	brain
25	chr6:117870400-117875000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:117870400-117876400	Weak transcription	NHLF	lung
27	chr6:117870400-117876600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:117870400-117879800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:117870400-117880000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:117870400-117880200	Weak transcription	Esophagus	oesophagus
31	chr6:117870400-117880400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:117870400-117883000	Weak transcription	Placenta	Placenta
33	chr6:117870400-117883800	Weak transcription	Brain Angular Gyrus	brain
34	chr6:117870400-117883800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:117870400-117884000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:117870400-117884000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:117870400-117884200	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:117870400-117884400	Weak transcription	Fetal Intestine Small	intestine
39	chr6:117870400-117886800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:117870400-117889600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr6:117870400-117889600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:117870600-117876600	Weak transcription	HepG2	liver
43	chr6:117870600-117879000	Weak transcription	GM12878-XiMat	blood
44	chr6:117870600-117880200	Weak transcription	Thymus	Thymus
45	chr6:117870600-117884000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr6:117870600-117884200	Weak transcription	Fetal Intestine Large	intestine
47	chr6:117870600-117886800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:117870800-117874400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:117871000-117877000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:117871000-117880200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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