Variant report

Variant	rs16879003
Chromosome Location	chr6:16745239-16745240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:16738254..16740721-chr6:16742412..16745248,2	MCF-7	breast:
2	chr6:16740481..16745919-chr6:16759194..16763421,5	MCF-7	breast:
3	chr6:16716594..16718951-chr6:16743535..16746274,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124788	Chromatin interaction
ENSG00000229931	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10434861	1.00[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs10456788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456789	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10456790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456791	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949379	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194640	0.86[CEU][hapmap];0.90[JPT][hapmap]
rs16878970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806144	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6459484	1.00[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs6915772	0.88[EUR][1000 genomes]
rs9350015	1.00[CEU][hapmap];0.90[TSI][hapmap]

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	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16879003	ATXN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16713800-16747800	Weak transcription	Brain Germinal Matrix	brain
2	chr6:16720200-16747800	Weak transcription	Fetal Brain Male	brain
3	chr6:16731600-16746000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:16732000-16745600	Weak transcription	Primary T cells from cord blood	blood
5	chr6:16732200-16746800	Weak transcription	Hela-S3	cervix
6	chr6:16732200-16754800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:16732600-16748000	Weak transcription	Colonic Mucosa	Colon
8	chr6:16736800-16748800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:16737400-16747400	Weak transcription	Fetal Brain Female	brain
10	chr6:16737600-16746600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:16737600-16747600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:16737600-16759400	Weak transcription	Thymus	Thymus
13	chr6:16738000-16749800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:16738200-16745600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:16738400-16745800	Weak transcription	Liver	Liver
16	chr6:16738600-16745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:16738600-16745800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:16739000-16752200	Weak transcription	HUVEC	blood vessel
19	chr6:16739800-16745600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:16739800-16748000	Weak transcription	Adipose Nuclei	Adipose
21	chr6:16740000-16747400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:16740200-16748000	Weak transcription	Right Ventricle	heart
23	chr6:16740800-16746600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:16741200-16747400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:16741200-16758200	Enhancers	Fetal Heart	heart
26	chr6:16741400-16746400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:16741400-16746600	Genic enhancers	HepG2	liver
28	chr6:16741400-16747000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr6:16741600-16747600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:16742000-16745400	Weak transcription	Fetal Kidney	kidney
31	chr6:16742000-16746800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:16742200-16747200	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:16742200-16747400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:16742600-16745400	Weak transcription	NHEK	skin
35	chr6:16742600-16745800	Weak transcription	Fetal Intestine Large	intestine
36	chr6:16742600-16747200	Weak transcription	HMEC	breast
37	chr6:16742600-16748200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:16742800-16745800	Weak transcription	Fetal Thymus	thymus
39	chr6:16742800-16745800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:16742800-16747200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:16742800-16747400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:16743000-16745400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:16743000-16745600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:16743000-16745800	Weak transcription	Small Intestine	intestine
45	chr6:16743000-16746800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:16743000-16747000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:16743000-16747200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:16743000-16747200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:16743000-16747200	Weak transcription	GM12878-XiMat	blood
50	chr6:16743000-16748000	Weak transcription	Ovary	ovary

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