Variant report

Variant	rs3746319
Chromosome Location	chr19:44612231-44612232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr19:44610811-44612494	HEK293	kidney:	n/a	n/a
2	CBX3	chr19:44611921-44612240	K562	blood:	n/a	n/a
3	MAX	chr19:44612027-44612449	K562	blood:	n/a	n/a
4	TCF12	chr19:44610675-44612588	A549	lung:	n/a	n/a
5	SETDB1	chr19:44610641-44613060	U2OS	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44611647..44614063-chr19:44614697..44617156,2	K562	blood:
2	chr17:58602968..58604763-chr19:44611791..44613959,2	MCF-7	breast:
3	chr19:44611565..44614380-chr19:44615671..44618988,4	MCF-7	breast:
4	chr19:44599467..44601264-chr19:44610771..44613313,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF235-4	chr19:44609492-44612490	NONHSAT066662
2	lnc-ZNF235-4	chr19:44609616-44612490	ENSG00000186019.10

No data

Variant related genes	Relation type
ZNF225	TF binding region
ENSG00000256294	Chromatin interaction
ENSG00000186019	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000267680	Chromatin interaction
ENSG00000062725	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10406335	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs10408901	0.91[CHB][hapmap]
rs10410306	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10413195	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs10420143	0.93[ASN][1000 genomes]
rs10853771	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1236715	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1236716	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2061332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061333	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284978	0.87[CHB][hapmap]
rs2284980	0.91[CHB][hapmap]
rs2284981	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28446946	0.92[ASN][1000 genomes]
rs28539456	0.92[ASN][1000 genomes]
rs3172	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3200505	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746321	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239529	0.91[CHB][hapmap]
rs4429390	0.91[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs4459653	0.91[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs4508518	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802204	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802205	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802206	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4802207	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802208	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4803676	0.91[CHB][hapmap]
rs4803678	0.87[CHB][hapmap]
rs4803680	0.86[CHB][hapmap]
rs4803681	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55876899	0.86[ASN][1000 genomes]
rs56353321	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62115524	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62115526	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7250004	0.93[ASN][1000 genomes]
rs7250005	0.91[ASN][1000 genomes]
rs7253485	0.83[EUR][1000 genomes]
rs7508149	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8099869	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8104573	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8105860	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8108021	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8108404	0.90[ASN][1000 genomes]
rs8113750	0.95[ASN][1000 genomes]
rs9304638	0.91[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3746319	CPT1C	cis	cerebellum	SCAN
rs3746319	ZNF221	cis	Lymphoblastoid	GTEx
rs3746319	ZNF224	Cis_1M	lymphoblastoid	RTeQTL
rs3746319	SIGLEC12	cis	parietal	SCAN
rs3746319	SNORD34	cis	parietal	SCAN
rs3746319	FUT2	cis	parietal	SCAN
rs3746319	APOE	cis	parietal	SCAN
rs3746319	SNRPD2	cis	cerebellum	SCAN
rs3746319	KLK10	cis	cerebellum	SCAN
rs3746319	CLPTM1	cis	cerebellum	SCAN
rs3746319	ZNF223	cis	Thyroid	GTEx
rs3746319	ZNF221	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44600400-44616200	ZNF genes & repeats	Liver	Liver
2	chr19:44600800-44612800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:44600800-44614000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:44600800-44614600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:44604200-44613000	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:44604600-44612800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:44604800-44612400	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr19:44604800-44616000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr19:44605200-44614600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:44605800-44612600	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr19:44605800-44613000	ZNF genes & repeats	Fetal Lung	lung
12	chr19:44606600-44616400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr19:44607000-44612600	ZNF genes & repeats	GM12878-XiMat	blood
14	chr19:44607000-44612800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:44607000-44612800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
16	chr19:44607000-44613000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:44607400-44612800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:44607800-44613000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr19:44608000-44612600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:44608000-44612600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
21	chr19:44608000-44612800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
22	chr19:44608000-44613000	ZNF genes & repeats	Brain Germinal Matrix	brain
23	chr19:44608200-44612400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:44608200-44612800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
25	chr19:44608200-44613000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:44608200-44613800	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr19:44608200-44614600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:44608200-44615800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:44608400-44612800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
30	chr19:44608400-44612800	ZNF genes & repeats	A549	lung
31	chr19:44608400-44614400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:44608400-44614600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr19:44608400-44616000	ZNF genes & repeats	Fetal Brain Female	brain
34	chr19:44608600-44612600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr19:44608600-44613200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:44608600-44615800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr19:44609200-44613000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:44609200-44613000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
39	chr19:44609200-44613200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
40	chr19:44609800-44612600	ZNF genes & repeats	HUVEC	blood vessel
41	chr19:44609800-44612800	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
42	chr19:44609800-44613000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr19:44610000-44612800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:44610200-44612400	ZNF genes & repeats	Fetal Intestine Large	intestine
45	chr19:44610200-44612600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:44610200-44612600	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr19:44610200-44612600	ZNF genes & repeats	Psoas Muscle	Psoas
48	chr19:44610200-44612800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
49	chr19:44610200-44612800	ZNF genes & repeats	Brain Anterior Caudate	brain
50	chr19:44610200-44612800	ZNF genes & repeats	Brain Hippocampus Middle	brain

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