Variant report

Variant	rs12946508
Chromosome Location	chr17:19952059-19952060
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	chr17:19950835..19953752-chr17:19957285..19959162,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1009082	1.00[CHB][hapmap]
rs10438824	1.00[CHB][hapmap]
rs12449662	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12449914	0.81[AMR][1000 genomes]
rs12450857	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12453720	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12936794	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12937327	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12944084	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947950	1.00[CHB][hapmap]
rs12949485	1.00[CHB][hapmap]
rs1544421	1.00[CHB][hapmap]
rs1638527	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1638528	0.81[CEU][hapmap]
rs169413	0.87[ASN][1000 genomes]
rs17604987	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17605101	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17668529	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17686622	1.00[CHB][hapmap]
rs17686839	1.00[CHB][hapmap]
rs17759041	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17759609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs1812934	1.00[CHB][hapmap]
rs203467	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs203475	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs203478	0.83[CEU][hapmap]
rs203480	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2107566	1.00[CHB][hapmap]
rs2108981	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2158473	1.00[CHB][hapmap]
rs2189710	1.00[CHB][hapmap]
rs2263175	1.00[CHB][hapmap]
rs2386485	1.00[CHB][hapmap]
rs2526460	1.00[CHB][hapmap]
rs2526462	1.00[CHB][hapmap]
rs2526471	1.00[CHB][hapmap]
rs2526474	1.00[CHB][hapmap]
rs2526475	1.00[CHB][hapmap]
rs2526480	1.00[CHB][hapmap]
rs2526484	1.00[CHB][hapmap]
rs2526491	1.00[CHB][hapmap]
rs2703772	1.00[CHB][hapmap]
rs2703773	1.00[CHB][hapmap]
rs2703774	1.00[CHB][hapmap]
rs2703782	1.00[CHB][hapmap]
rs2703794	1.00[CHB][hapmap]
rs2703799	1.00[CHB][hapmap]
rs2703801	1.00[CHB][hapmap]
rs2703802	1.00[CHB][hapmap]
rs2703804	1.00[CHB][hapmap]
rs2703806	1.00[CHB][hapmap]
rs2703808	1.00[CHB][hapmap]
rs2703813	1.00[CHB][hapmap]
rs2703815	1.00[CHB][hapmap]
rs2703816	1.00[CHB][hapmap]
rs2703817	1.00[CHB][hapmap]
rs2703818	1.00[CHB][hapmap]
rs2703821	1.00[CHB][hapmap]
rs34089239	1.00[CHB][hapmap]
rs34182788	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34726000	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35254155	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35315252	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35317166	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35915823	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35925051	0.82[AMR][1000 genomes]
rs35979784	0.87[ASN][1000 genomes]
rs36097967	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3862151	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4577147	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588033	1.00[CHB][hapmap]
rs4924802	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4924809	1.00[CHB][hapmap]
rs4924810	1.00[CHB][hapmap]
rs4925054	1.00[CHB][hapmap]
rs4925063	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4925064	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4925071	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4925074	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4925084	1.00[CHB][hapmap]
rs56005410	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56371654	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62066345	0.82[AMR][1000 genomes]
rs62066346	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62066347	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62066348	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62066349	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62066350	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62066351	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62067482	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067483	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209653	0.86[CEU][hapmap]
rs8079923	0.82[CEU][hapmap];0.87[ASN][1000 genomes]
rs850622	0.82[CEU][hapmap]
rs9901294	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12946508	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19923400-19956600	Weak transcription	A549	lung
2	chr17:19932000-19956800	Weak transcription	Ovary	ovary
3	chr17:19943800-19965800	Weak transcription	Aorta	Aorta
4	chr17:19945800-19956000	Weak transcription	K562	blood
5	chr17:19947000-19953000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:19948200-19966400	Weak transcription	Brain Angular Gyrus	brain
7	chr17:19949400-19953200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:19950800-19966400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:19951200-19956800	Weak transcription	Left Ventricle	heart

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