Variant report

Variant	rs3213255
Chromosome Location	chr19:44077507-44077508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44077485-44077789	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44076409..44078057-chr19:44100171..44102190,2	MCF-7	breast:
2	chr19:44076171..44077676-chr19:44133268..44135253,2	K562	blood:
3	chr19:44065444..44067870-chr19:44076256..44078138,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269583	TF binding region
PINLYP	TF binding region
ENSG00000167378	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000124444	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10402946	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs12983281	0.82[ASN][1000 genomes]
rs1475933	0.82[ASN][1000 genomes]
rs17655646	0.81[CHB][hapmap]
rs184239	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1978008	0.97[ASN][1000 genomes]
rs2030404	0.89[ASW][hapmap];0.85[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2139720	0.83[ASN][1000 genomes]
rs25479	0.82[ASN][1000 genomes]
rs25485	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2599461	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2599462	0.89[ASW][hapmap];0.85[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2682547	0.84[CEU][hapmap]
rs2682563	0.85[CEU][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs2682585	0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2682586	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2854500	0.86[ASN][1000 genomes]
rs2854501	0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2854506	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2854507	0.97[ASN][1000 genomes]
rs2854508	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2854509	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs304731	0.81[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs3213263	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213276	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213295	0.84[ASN][1000 genomes]
rs3213329	0.82[ASN][1000 genomes]
rs3213333	0.86[ASN][1000 genomes]
rs3213334	0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3213356	0.89[ASW][hapmap];0.85[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3213387	0.82[ASN][1000 genomes]
rs34704825	0.84[ASN][1000 genomes]
rs3547	0.82[ASN][1000 genomes]
rs4803646	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs7251275	0.90[CHB][hapmap]
rs73043690	0.82[ASN][1000 genomes]
rs762506	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs762507	0.85[CEU][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs915927	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1063149	chr19:44059081-44087583	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs3213255	TRPM4	cis	cerebellum	SCAN
rs3213255	ZNF575	cis	Nerve Tibial	GTEx
rs3213255	SLC17A7	cis	cerebellum	SCAN
rs3213255	ZNF575	cis	lung	GTEx
rs3213255	XRCC1	cis	lymphoblastoid	seeQTL
rs3213255	XRCC1	cis	Thyroid	GTEx
rs3213255	SLC1A5	cis	cerebellum	SCAN
rs3213255	IZUMO1	cis	cerebellum	SCAN
rs3213255	CD37	cis	parietal	SCAN
rs3213255	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs3213255	BCAT2	cis	cerebellum	SCAN
rs3213255	ZNF575	cis	Adipose Subcutaneous	GTEx
rs3213255	XRCC1	cis	multi-tissue	Pritchard
rs3213255	GRIN2D	cis	parietal	SCAN
rs3213255	XRCC1	cis	Liver	GTEx
rs3213255	BLOC1S3	cis	parietal	SCAN
rs3213255	ZNF229	cis	multi-tissue	Pritchard
rs3213255	BCAT2	cis	parietal	SCAN
rs3213255	ZNF575	cis	Artery Tibial	GTEx
rs3213255	ZNF649	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44039200-44078600	Weak transcription	Hela-S3	cervix
2	chr19:44048400-44078800	Weak transcription	Small Intestine	intestine
3	chr19:44057800-44078800	Weak transcription	HSMMtube	muscle
4	chr19:44058600-44078800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:44059200-44078800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:44059800-44078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:44065200-44078600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:44065400-44078600	Weak transcription	Ovary	ovary
9	chr19:44065400-44078800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:44065400-44078800	Weak transcription	Aorta	Aorta
11	chr19:44065800-44078600	Weak transcription	HSMM	muscle
12	chr19:44066000-44078600	Weak transcription	K562	blood
13	chr19:44066200-44078800	Weak transcription	Pancreas	Pancrea
14	chr19:44066600-44078800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:44067000-44078600	Weak transcription	Gastric	stomach
16	chr19:44067200-44078600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr19:44067200-44078600	Weak transcription	Fetal Kidney	kidney
18	chr19:44067400-44078600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:44067400-44078600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:44067400-44078600	Weak transcription	Liver	Liver
21	chr19:44067400-44078600	Weak transcription	Brain Substantia Nigra	brain
22	chr19:44067400-44078600	Weak transcription	Left Ventricle	heart
23	chr19:44067400-44078600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:44067400-44078600	Weak transcription	HUVEC	blood vessel
25	chr19:44067400-44078800	Weak transcription	Fetal Heart	heart
26	chr19:44067400-44078800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr19:44067400-44078800	Weak transcription	Right Ventricle	heart
28	chr19:44067600-44078800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:44067800-44077600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:44067800-44078600	Weak transcription	Esophagus	oesophagus
31	chr19:44068000-44078600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:44068000-44078600	Weak transcription	Brain Angular Gyrus	brain
33	chr19:44068000-44078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:44068000-44078600	Weak transcription	Spleen	Spleen
35	chr19:44068000-44078600	Weak transcription	NH-A	brain
36	chr19:44068000-44078800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:44068000-44078800	Weak transcription	Lung	lung
38	chr19:44068200-44077800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:44068200-44078600	Weak transcription	Brain Hippocampus Middle	brain
40	chr19:44068200-44078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:44068200-44078800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:44068200-44078800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr19:44068400-44078600	Weak transcription	Colon Smooth Muscle	Colon
44	chr19:44068600-44078600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:44068600-44078600	Weak transcription	Fetal Lung	lung
46	chr19:44068600-44078800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr19:44068600-44078800	Weak transcription	Fetal Intestine Large	intestine
48	chr19:44068800-44078600	Weak transcription	HepG2	liver
49	chr19:44069200-44078600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:44069400-44078600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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