Variant report

Variant	rs17034560
Chromosome Location	chr1:10229158-10229159
allele	A/G
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	YY1	chr1:10228960-10229371	GM12892	blood:	n/a	n/a
2	MYBL2	chr1:10229149-10229953	HepG2	liver:	n/a	n/a
3	YY1	chr1:10228882-10229449	GM12878	blood:	n/a	n/a
4	YY1	chr1:10228968-10229592	GM12878	blood:	n/a	n/a
5	FOXA1	chr1:10229021-10229918	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:10228971-10229542	GM12892	blood:	n/a	n/a
7	YY1	chr1:10228963-10229162	K562	blood:	n/a	n/a
8	FOXA2	chr1:10228970-10230087	HepG2	liver:	n/a	n/a
9	RCOR1	chr1:10229091-10229650	HepG2	liver:	n/a	n/a
10	RUNX3	chr1:10228917-10229477	GM12878	blood:	n/a	n/a
11	YY1	chr1:10228965-10229359	GM12892	blood:	n/a	n/a
12	BHLHE40	chr1:10229112-10229223	GM12878	blood:	n/a	n/a
13	FOXA2	chr1:10228950-10229881	HepG2	liver:	n/a	n/a
14	ARID3A	chr1:10229143-10229923	HepG2	liver:	n/a	n/a
15	FOXA1	chr1:10228911-10229871	HepG2	liver:	n/a	n/a
16	FOXA1	chr1:10229014-10229883	HepG2	liver:	n/a	n/a
17	BATF	chr1:10228993-10229393	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:10229138-10229178	K562	blood:	n/a	n/a
19	FOXA1	chr1:10229061-10229847	HepG2	liver:	n/a	n/a
20	RUNX3	chr1:10228997-10229470	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
UBE4B	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11803995	0.83[TSI][hapmap]
rs12045943	0.92[GIH][hapmap]
rs12070814	0.81[JPT][hapmap]
rs12076922	0.81[JPT][hapmap]
rs12092513	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17034545	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17034558	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2273298	0.84[CHD][hapmap]
rs2273299	0.84[CHD][hapmap]
rs61782920	0.95[EUR][1000 genomes]
rs61782925	0.89[ASN][1000 genomes]
rs61782926	0.91[ASN][1000 genomes]
rs61782927	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61782933	1.00[ASN][1000 genomes]
rs61782936	1.00[ASN][1000 genomes]
rs61782937	1.00[ASN][1000 genomes]
rs61782938	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667049	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs6673887	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs6685910	0.81[JPT][hapmap]
rs6687550	0.92[GIH][hapmap];0.81[JPT][hapmap]
rs6692491	0.80[ASN][1000 genomes]
rs6700518	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17034560	BMPR2	trans	brain	seeQTL
rs17034560	NEMF	trans	brain	seeQTL
rs17034560	MAP3K5	trans	brain	seeQTL
rs17034560	LZIC	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10182200-10231200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:10182400-10229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:10182800-10231400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:10184000-10235000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:10191200-10239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:10193200-10231200	Weak transcription	Small Intestine	intestine
7	chr1:10194200-10232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:10195600-10231200	Weak transcription	HUVEC	blood vessel
9	chr1:10201600-10231200	Weak transcription	HMEC	breast
10	chr1:10211200-10236400	Strong transcription	Fetal Stomach	stomach
11	chr1:10213200-10231000	Weak transcription	A549	lung
12	chr1:10213800-10236000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:10214600-10235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:10214600-10237000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:10215200-10229200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:10215400-10234400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:10216200-10236400	Strong transcription	Placenta	Placenta
18	chr1:10217800-10230200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:10218000-10234600	Strong transcription	Liver	Liver
20	chr1:10218200-10229600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:10218200-10235800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr1:10218200-10236600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:10218400-10236200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:10219800-10229600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:10219800-10234000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:10220000-10230200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:10220000-10233800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:10221000-10236400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:10221000-10236600	Strong transcription	Adipose Nuclei	Adipose
30	chr1:10221200-10230400	Strong transcription	Fetal Intestine Small	intestine
31	chr1:10221600-10229800	Strong transcription	Fetal Intestine Large	intestine
32	chr1:10221800-10242200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:10222000-10236000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:10222200-10236400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:10223000-10235000	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:10223000-10237800	Weak transcription	Psoas Muscle	Psoas
37	chr1:10224400-10233400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:10224400-10233400	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr1:10224400-10235000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:10224400-10235600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:10224400-10236600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:10224600-10230600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:10224800-10229200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:10224800-10234200	Strong transcription	Fetal Brain Female	brain
45	chr1:10224800-10236600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:10225000-10230200	Strong transcription	Aorta	Aorta
47	chr1:10225800-10231200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:10226000-10232600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:10226000-10232600	Weak transcription	Fetal Heart	heart
50	chr1:10226400-10229200	Weak transcription	HSMM	muscle

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