Variant report

Variant	rs891666
Chromosome Location	chr3:150827190-150827191
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150824339..150827241-chr3:150830222..150833263,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10513390	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1220996	0.81[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1221001	0.81[AMR][1000 genomes]
rs1221005	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1231521	1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs12497969	1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1554121	0.89[CEU][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2043171	0.80[EUR][1000 genomes]
rs2048229	0.91[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2116290	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2567322	0.83[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2700471	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2700473	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2700474	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35995638	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4680058	1.00[YRI][hapmap]
rs7629773	0.83[ASW][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs977423	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9942131	0.83[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915879	chr3:150607390-150860207	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs891666	HLTF	cis	parietal	SCAN
rs891666	MBNL1	cis	parietal	SCAN
rs891666	GPR149	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150809800-150827400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:150819800-150827600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:150819800-150847600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:150820800-150840000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:150823200-150843000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:150825000-150827200	Enhancers	Placenta	Placenta
7	chr3:150825200-150827400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:150825200-150828200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:150825800-150828000	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:150825800-150829000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:150826000-150831600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:150826000-150855200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:150826400-150827200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:150826400-150827200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:150826400-150827600	Active TSS	Ovary	ovary
16	chr3:150826400-150830600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:150826400-150863600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:150826600-150827400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:150826600-150827800	Weak transcription	Fetal Intestine Small	intestine
20	chr3:150826600-150830200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:150826600-150830200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:150826600-150830800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:150826600-150846400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:150826600-150851800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:150826600-150855000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:150826800-150827200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:150826800-150830600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:150826800-150841600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:150826800-150846600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:150827000-150827200	Active TSS	HepG2	liver
31	chr3:150827000-150827400	Active TSS	Brain Anterior Caudate	brain
32	chr3:150827000-150827600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:150827000-150827800	Enhancers	Fetal Intestine Large	intestine

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