Variant report

Variant	rs888423
Chromosome Location	chr17:19999409-19999410
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	chr17:19912973..19913861-chr17:19998764..19999738,2	K562	blood:
2	chr17:19912162..19913083-chr17:19998469..19999472,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction
ENSG00000261033	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10083856	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034904	0.83[AMR][1000 genomes]
rs10491107	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs11867585	1.00[CEU][hapmap];0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868084	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868116	0.82[EUR][1000 genomes]
rs11869616	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11870111	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871651	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs119672	0.94[CHB][hapmap]
rs12603372	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs12936443	0.82[EUR][1000 genomes]
rs12942179	0.88[CEU][hapmap]
rs1479129	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs1638525	0.86[CHB][hapmap]
rs169412	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs16960697	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs175922	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs1859407	0.81[EUR][1000 genomes]
rs1860302	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs2013443	0.82[EUR][1000 genomes]
rs203450	0.94[CHB][hapmap]
rs203457	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs203458	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs203460	0.94[CHB][hapmap]
rs203462	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs203465	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs203466	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs203477	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs203479	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs203481	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs2042046	0.85[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2107565	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2108978	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs2108979	0.80[AMR][1000 genomes]
rs2108980	0.83[AMR][1000 genomes]
rs2189709	0.81[EUR][1000 genomes]
rs2526463	0.81[EUR][1000 genomes]
rs2526466	0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs2526476	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2526477	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2526478	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2703771	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2703776	0.85[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs2703795	0.80[EUR][1000 genomes]
rs2703800	0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2703805	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2703807	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs2703814	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs28603224	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637614	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28666381	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28807825	0.85[AMR][1000 genomes]
rs34290687	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34291370	0.81[AMR][1000 genomes]
rs34401389	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35003563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313716	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36077949	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862152	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888318	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909258	0.85[AMR][1000 genomes]
rs397969	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs4005937	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4267380	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4479309	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4570919	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924801	0.83[AMR][1000 genomes]
rs4924803	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924806	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925060	0.87[CHB][hapmap]
rs4925065	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes]
rs4925066	0.83[AMR][1000 genomes]
rs4925067	0.83[AMR][1000 genomes]
rs4925069	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4925072	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925073	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925079	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925081	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925085	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925086	0.82[EUR][1000 genomes]
rs4925087	0.82[EUR][1000 genomes]
rs4925090	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs4925091	0.80[EUR][1000 genomes]
rs55705283	0.82[EUR][1000 genomes]
rs62066865	0.82[EUR][1000 genomes]
rs62066870	0.80[EUR][1000 genomes]
rs62067555	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587219	0.82[EUR][1000 genomes]
rs7207625	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208025	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208365	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208635	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209734	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7211535	0.80[AMR][1000 genomes]
rs7212500	0.81[EUR][1000 genomes]
rs7216599	0.81[EUR][1000 genomes]
rs7216794	0.81[EUR][1000 genomes]
rs7219908	0.81[EUR][1000 genomes]
rs7222403	0.94[CHB][hapmap]
rs7222984	0.82[EUR][1000 genomes]
rs7222987	0.80[EUR][1000 genomes]
rs7223305	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757494	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs8065337	0.82[AMR][1000 genomes]
rs8066143	0.81[EUR][1000 genomes]
rs8067545	0.81[AMR][1000 genomes]
rs8078716	0.81[EUR][1000 genomes]
rs8080649	0.80[EUR][1000 genomes]
rs850623	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs860335	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs918227	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs918228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889743	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9891739	0.85[AMR][1000 genomes]
rs9893832	0.85[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9896411	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897246	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897653	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898080	0.82[EUR][1000 genomes]
rs9901336	0.80[EUR][1000 genomes]
rs9902032	0.82[EUR][1000 genomes]
rs9907788	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9912775	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915758	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9944451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs888423	CYTSB	cis	cerebellum	SCAN
rs888423	MTO1	trans	cerebellum	SCAN
rs888423	TMEM11	cis	cerebellum	SCAN
rs888423	AKAP10	cis	lymphoblastoid	seeQTL
rs888423	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs888423	AKAP10	cis	Lymphoblastoid	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:19993800-20001600	Weak transcription	Lung	lung
7	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
8	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
9	chr17:19995000-20000000	Weak transcription	Right Ventricle	heart
10	chr17:19995000-20001200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:19996600-20000800	Weak transcription	Aorta	Aorta
12	chr17:19996800-19999600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr17:19997600-19999600	Enhancers	Fetal Muscle Leg	muscle
14	chr17:19998200-20000000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr17:19998200-20000000	Enhancers	Brain Substantia Nigra	brain
16	chr17:19998600-20000400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr17:19998800-20000600	Enhancers	Ovary	ovary
18	chr17:19999000-19999600	Enhancers	Brain Angular Gyrus	brain
19	chr17:19999000-19999800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:19999000-19999800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr17:19999000-20000200	Enhancers	Adipose Nuclei	Adipose
22	chr17:19999000-20002400	Weak transcription	Gastric	stomach
23	chr17:19999000-20006000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr17:19999200-20000000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:19999200-20000000	Weak transcription	Right Atrium	heart
27	chr17:19999200-20000200	Enhancers	Brain Cingulate Gyrus	brain
28	chr17:19999200-20000200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr17:19999200-20000400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:19999200-20001400	Weak transcription	Spleen	Spleen
31	chr17:19999200-20001800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr17:19999200-20002000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr17:19999200-20002600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr17:19999200-20005000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr17:19999200-20008800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:19999400-19999800	Enhancers	Brain Hippocampus Middle	brain
37	chr17:19999400-20000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:19999400-20000400	Enhancers	Brain Anterior Caudate	brain
39	chr17:19999400-20000400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr17:19999400-20004400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr17:19999400-20005000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:19999400-20005600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:19999400-20011800	Weak transcription	A549	lung

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