Variant report

Variant	rs1156869
Chromosome Location	chr9:6418000-6418001
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr9:6417329-6418130	GM12878	blood:	n/a	n/a
2	NFIC	chr9:6417142-6418147	GM12878	blood:	n/a	n/a
3	IKZF1	chr9:6417629-6418318	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:6412902..6414944-chr9:6415944..6418989,4	MCF-7	breast:
2	chr9:6417024..6418829-chr9:6426585..6429333,3	K562	blood:
3	chr9:6417292..6420636-chr9:6422611..6425827,4	K562	blood:
4	chr9:6417367..6418926-chr9:6465280..6467264,2	MCF-7	breast:
5	chr9:6417900..6420636-chr9:6424327..6426106,2	K562	blood:
6	chr9:6412634..6415362-chr9:6415861..6419998,11	K562	blood:

No data

Variant related genes	Relation type
UHRF2	TF binding region
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10115294	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10119350	1.00[JPT][hapmap]
rs10123132	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10123605	0.96[EUR][1000 genomes]
rs10125053	1.00[CEU][hapmap]
rs10125090	1.00[CEU][hapmap]
rs10125313	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1037885	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1048279	0.88[EUR][1000 genomes]
rs10491838	1.00[EUR][1000 genomes]
rs10739096	0.96[EUR][1000 genomes]
rs10739101	1.00[EUR][1000 genomes]
rs10739103	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10739104	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758762	0.91[EUR][1000 genomes]
rs10758763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs10758768	0.96[EUR][1000 genomes]
rs10815400	0.96[EUR][1000 genomes]
rs10815401	0.96[EUR][1000 genomes]
rs10815429	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10815430	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10815441	1.00[YRI][hapmap]
rs10975501	0.85[CEU][hapmap]
rs12346381	0.88[EUR][1000 genomes]
rs1322170	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13283464	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13283631	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13283687	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs13284032	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13284392	0.87[EUR][1000 genomes]
rs13285125	0.83[EUR][1000 genomes]
rs13285152	0.96[EUR][1000 genomes]
rs13285458	0.96[EUR][1000 genomes]
rs13286720	1.00[YRI][hapmap]
rs13288875	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13290126	1.00[YRI][hapmap]
rs13290488	0.83[EUR][1000 genomes]
rs13291494	0.96[EUR][1000 genomes]
rs13291887	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13292030	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13293015	0.92[EUR][1000 genomes]
rs13293673	0.84[EUR][1000 genomes]
rs13294924	0.83[EUR][1000 genomes]
rs13296481	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs13296692	0.83[EUR][1000 genomes]
rs13298872	0.96[EUR][1000 genomes]
rs13299896	0.96[EUR][1000 genomes]
rs13300059	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13302032	0.96[EUR][1000 genomes]
rs1330381	0.96[EUR][1000 genomes]
rs1381038	0.91[EUR][1000 genomes]
rs1407357	0.91[EUR][1000 genomes]
rs1407358	0.91[EUR][1000 genomes]
rs1412420	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs1563	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16924678	1.00[YRI][hapmap]
rs16924682	1.00[YRI][hapmap]
rs1854709	0.85[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs1855022	0.84[EUR][1000 genomes]
rs2000198	0.88[EUR][1000 genomes]
rs2019737	0.91[EUR][1000 genomes]
rs2051003	0.88[EUR][1000 genomes]
rs2150964	0.81[EUR][1000 genomes]
rs2150971	0.88[EUR][1000 genomes]
rs2282158	1.00[YRI][hapmap]
rs2297443	1.00[YRI][hapmap]
rs2381438	0.84[EUR][1000 genomes]
rs28615746	0.96[EUR][1000 genomes]
rs2890707	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs34530211	0.96[EUR][1000 genomes]
rs34581400	0.96[EUR][1000 genomes]
rs35301257	0.96[EUR][1000 genomes]
rs35408061	0.96[EUR][1000 genomes]
rs36089474	0.96[EUR][1000 genomes]
rs3818705	1.00[YRI][hapmap]
rs3847262	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3858051	0.91[EUR][1000 genomes]
rs4008347	0.96[EUR][1000 genomes]
rs424119	1.00[EUR][1000 genomes]
rs4475552	0.84[EUR][1000 genomes]
rs4742172	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4742177	0.91[EUR][1000 genomes]
rs4742180	0.96[EUR][1000 genomes]
rs4742198	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742200	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742203	1.00[EUR][1000 genomes]
rs503315	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs553048	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs6477060	0.88[EUR][1000 genomes]
rs6477067	0.91[EUR][1000 genomes]
rs67541153	0.91[EUR][1000 genomes]
rs67797327	0.83[EUR][1000 genomes]
rs7021445	0.96[EUR][1000 genomes]
rs7031407	0.96[EUR][1000 genomes]
rs7031967	0.92[EUR][1000 genomes]
rs7035574	0.88[EUR][1000 genomes]
rs7036990	0.91[EUR][1000 genomes]
rs7039968	0.91[EUR][1000 genomes]
rs7040374	0.88[EUR][1000 genomes]
rs7041863	1.00[CEU][hapmap]
rs7043824	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043887	0.96[EUR][1000 genomes]
rs7044749	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045164	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7048431	0.84[EUR][1000 genomes]
rs72693587	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7350177	0.96[EUR][1000 genomes]
rs7851921	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7852138	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7853322	0.92[EUR][1000 genomes]
rs7858373	0.91[EUR][1000 genomes]
rs7859139	0.91[EUR][1000 genomes]
rs7864212	0.91[EUR][1000 genomes]
rs7869419	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7873206	0.96[EUR][1000 genomes]
rs898673	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs922221	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs980849	0.96[EUR][1000 genomes]
rs980850	0.88[EUR][1000 genomes]
rs993952	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS 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	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS 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	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1156869	UHRF2	Cis_1M	lymphoblastoid	RTeQTL
rs1156869	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:139 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414400-6427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:6414600-6439400	Weak transcription	Colonic Mucosa	Colon
3	chr9:6414600-6449000	Weak transcription	Gastric	stomach
4	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
6	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
7	chr9:6414800-6422000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:6415400-6418800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:6415400-6418800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:6415400-6419400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr9:6415400-6419600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:6415400-6419600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr9:6415400-6425400	Weak transcription	Psoas Muscle	Psoas
14	chr9:6415400-6434000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:6415600-6418000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:6415600-6418600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:6415600-6418600	Weak transcription	Adipose Nuclei	Adipose
18	chr9:6415600-6419200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:6415600-6419400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:6415600-6419400	Enhancers	Primary B cells from cord blood	blood
21	chr9:6415600-6420800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:6415600-6421000	Weak transcription	Fetal Intestine Large	intestine
23	chr9:6415600-6422000	Weak transcription	Fetal Kidney	kidney
24	chr9:6415600-6422200	Weak transcription	Lung	lung
25	chr9:6415600-6423200	Weak transcription	Stomach Mucosa	stomach
26	chr9:6415600-6430000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:6415600-6431000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
30	chr9:6415800-6419400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:6416000-6418000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:6416000-6420000	Weak transcription	Fetal Intestine Small	intestine
34	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:6416200-6418800	Weak transcription	Right Atrium	heart
36	chr9:6416200-6418800	Active TSS	GM12878-XiMat	blood
37	chr9:6416200-6419200	Enhancers	Brain Cingulate Gyrus	brain
38	chr9:6416200-6419800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:6416400-6418600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr9:6416400-6419000	Enhancers	Fetal Brain Male	brain
41	chr9:6416400-6420600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:6416400-6421400	Weak transcription	Left Ventricle	heart
43	chr9:6416400-6421400	Weak transcription	Pancreas	Pancrea
44	chr9:6416400-6429800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:6416400-6430000	Weak transcription	Spleen	Spleen
46	chr9:6416400-6430600	Weak transcription	Right Ventricle	heart
47	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:6416600-6418200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr9:6416600-6419000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:6416600-6419400	Enhancers	Primary B cells from peripheral blood	blood

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