Variant report

Variant	rs427608
Chromosome Location	chr19:44512624-44512625
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44438985..44440520-chr19:44510451..44513064,2	MCF-7	breast:
2	chr19:44506929..44508722-chr19:44508906..44512991,6	K562	blood:
3	chr19:44505048..44507661-chr19:44511684..44514598,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124459	Chromatin interaction
ENSG00000266921	Chromatin interaction
ENSG00000159882	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11083734	0.89[ASN][1000 genomes]
rs11083735	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083736	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083737	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11666432	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12610472	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1474061	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996409	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2138823	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2138824	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2176431	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs382197	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3826941	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4239528	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4299256	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4371266	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4375771	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4444434	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs451388	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs454904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4550576	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4555257	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803668	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803672	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803674	0.91[CHB][hapmap];0.81[MEX][hapmap]
rs55798868	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56003307	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56230322	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56250154	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57895932	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62115491	0.82[ASN][1000 genomes]
rs62119177	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509135	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509137	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7251015	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7252213	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7255192	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7257809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105003	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8109313	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8109615	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110348	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9646633	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv961225	chr19:44512566-44513320	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs427608	ZNF223	cis	Thyroid	GTEx
rs427608	FUT2	cis	parietal	SCAN
rs427608	OPA3	cis	parietal	SCAN
rs427608	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs427608	NTN5	cis	parietal	SCAN
rs427608	ZNF223	cis	Adipose Subcutaneous	GTEx
rs427608	ASPDH	cis	cerebellum	SCAN
rs427608	KPTN	cis	parietal	SCAN
rs427608	ZNF613	cis	parietal	SCAN
rs427608	ZNF223	cis	Nerve Tibial	GTEx
rs427608	ETFB	cis	parietal	SCAN
rs427608	APOC2	cis	parietal	SCAN
rs427608	HIF3A	cis	parietal	SCAN
rs427608	EMP3	cis	parietal	SCAN
rs427608	SPHK2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44508200-44512800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:44508400-44512800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr19:44508400-44513000	Weak transcription	K562	blood
4	chr19:44508400-44513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:44508400-44513600	Weak transcription	Hela-S3	cervix
6	chr19:44509200-44520600	ZNF genes & repeats	Liver	Liver
7	chr19:44509400-44516800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr19:44509400-44518200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:44509800-44516600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
10	chr19:44509800-44517000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:44509800-44517400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr19:44510000-44517000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
13	chr19:44510000-44517000	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr19:44510000-44517200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:44510000-44517400	ZNF genes & repeats	Primary T cells from cord blood	blood
16	chr19:44510200-44513000	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:44510200-44516600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
18	chr19:44510200-44517000	ZNF genes & repeats	GM12878-XiMat	blood
19	chr19:44510200-44517400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr19:44510200-44517600	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr19:44510400-44516400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:44510400-44517200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
23	chr19:44510400-44517600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:44510400-44517600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
25	chr19:44510600-44513200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:44510600-44513600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:44510600-44514400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:44510600-44516200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
29	chr19:44510600-44516600	ZNF genes & repeats	Fetal Muscle Leg	muscle
30	chr19:44510600-44516600	ZNF genes & repeats	A549	lung
31	chr19:44510600-44517000	ZNF genes & repeats	Fetal Lung	lung
32	chr19:44510600-44517400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr19:44510600-44517600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr19:44510800-44512800	Strong transcription	Rectal Smooth Muscle	rectum
35	chr19:44510800-44513600	Strong transcription	Osteobl	bone
36	chr19:44510800-44516400	ZNF genes & repeats	Dnd41	blood
37	chr19:44510800-44516600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr19:44510800-44516600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
39	chr19:44510800-44516600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
40	chr19:44510800-44516800	ZNF genes & repeats	Brain Substantia Nigra	brain
41	chr19:44510800-44517000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
42	chr19:44510800-44517200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr19:44510800-44517200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:44511000-44512800	Strong transcription	Gastric	stomach
45	chr19:44511000-44513400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:44511000-44514200	Strong transcription	Brain Angular Gyrus	brain
47	chr19:44511000-44515400	ZNF genes & repeats	Aorta	Aorta
48	chr19:44511000-44515600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:44511000-44515600	ZNF genes & repeats	Spleen	Spleen
50	chr19:44511000-44515800	ZNF genes & repeats	Esophagus	oesophagus

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