Variant report

Variant	rs12450857
Chromosome Location	chr17:19895248-19895249
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	chr17:19895147..19897764-chr17:19911354..19913515,3	K562	blood:
2	chr17:19894457..19896275-chr17:19994382..19996657,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261033	Chromatin interaction
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1009082	1.00[CHB][hapmap]
rs10438824	1.00[CHB][hapmap]
rs12449662	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936794	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12943369	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12944084	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12946508	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12947950	1.00[CHB][hapmap]
rs12949485	1.00[CHB][hapmap]
rs1638526	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1638527	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1638528	0.90[CEU][hapmap];0.84[AMR][1000 genomes]
rs169413	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604987	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17605101	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668529	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17686622	1.00[CHB][hapmap]
rs17686839	1.00[CHB][hapmap]
rs17759609	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1812934	1.00[CHB][hapmap]
rs203449	0.81[AMR][1000 genomes]
rs203454	0.82[AMR][1000 genomes]
rs203464	0.81[AMR][1000 genomes]
rs203467	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs203474	0.84[EUR][1000 genomes]
rs203475	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203476	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs203478	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs203480	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2108981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189710	1.00[CHB][hapmap]
rs2386485	1.00[CHB][hapmap]
rs2526460	1.00[CHB][hapmap]
rs2526462	1.00[CHB][hapmap]
rs2703794	1.00[CHB][hapmap]
rs2703799	1.00[CHB][hapmap]
rs34089239	1.00[CHB][hapmap]
rs34182788	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726000	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35254155	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35315252	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35925051	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35979784	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097967	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862151	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs427033	0.87[CEU][hapmap]
rs4577147	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4588033	1.00[CHB][hapmap]
rs4924802	1.00[CHB][hapmap]
rs4924809	1.00[CHB][hapmap]
rs4924810	1.00[CHB][hapmap]
rs4925054	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4925063	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925064	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925084	1.00[CHB][hapmap]
rs56005410	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066345	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62066346	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066347	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066348	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066349	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066350	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066351	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066352	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62067482	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62067483	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6813	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs7209653	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8079923	0.91[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs850622	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9891503	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9901294	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3382860	chr17:19894909-19918588	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12450857	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19890600-19899800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr17:19890800-19896400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr17:19890800-19899400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr17:19890800-19899800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:19890800-19899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:19891400-19896400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:19891600-19899800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr17:19891800-19896400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:19892000-19896400	Weak transcription	K562	blood
10	chr17:19893800-19895800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:19894200-19895600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:19894800-19896200	Weak transcription	Hela-S3	cervix
13	chr17:19894800-19896400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:19895000-19895400	Weak transcription	Brain Anterior Caudate	brain
15	chr17:19895000-19896200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:19895000-19896200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr17:19895000-19896200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:19895000-19896200	Weak transcription	A549	lung
19	chr17:19895000-19896400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:19895000-19896400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:19895000-19896400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:19895200-19896200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:19895200-19896200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:19895200-19896200	Weak transcription	Brain Hippocampus Middle	brain
25	chr17:19895200-19896200	Weak transcription	Brain Substantia Nigra	brain

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