Variant report

Variant	rs4742198
Chromosome Location	chr9:6419653-6419654
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:6412168..6415418-chr9:6418500..6425043,7	MCF-7	breast:
2	chr9:6417292..6420636-chr9:6422611..6425827,4	K562	blood:
3	chr9:6417900..6420636-chr9:6424327..6426106,2	K562	blood:
4	chr9:6412634..6415362-chr9:6415861..6419998,11	K562	blood:

Variant related genes	Relation type
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

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	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10491838	0.93[AMR][1000 genomes];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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739104	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][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];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10758768	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815400	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815401	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10815429	0.90[AFR][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]
rs1156869	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]
rs12346381	0.88[EUR][1000 genomes]
rs1322170	0.90[AFR][1000 genomes];1.00[AMR][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];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13284032	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13284392	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13285125	0.83[EUR][1000 genomes]
rs13285152	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13285458	0.93[AMR][1000 genomes];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	0.93[AMR][1000 genomes];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	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13293673	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13294924	0.83[EUR][1000 genomes]
rs13296481	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13296692	0.83[EUR][1000 genomes]
rs13298872	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299896	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13300059	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13302032	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1330381	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1381038	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1407357	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1407358	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1412420	0.85[CEU][hapmap];0.86[AMR][1000 genomes];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];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1855022	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2000198	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2019737	0.91[EUR][1000 genomes]
rs2051003	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2150964	0.81[EUR][1000 genomes]
rs2150971	0.86[AMR][1000 genomes];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	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34581400	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35301257	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35408061	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36089474	0.93[AMR][1000 genomes];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	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs424119	0.87[AMR][1000 genomes];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	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4742200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs503315	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs553048	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6477060	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6477067	0.91[EUR][1000 genomes]
rs67541153	0.91[EUR][1000 genomes]
rs67797327	0.83[EUR][1000 genomes]
rs7021445	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7031407	0.96[EUR][1000 genomes]
rs7031967	0.92[EUR][1000 genomes]
rs7032411	0.93[AMR][1000 genomes]
rs7035574	0.88[EUR][1000 genomes]
rs7036990	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7039968	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7040374	0.93[AMR][1000 genomes];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[AMR][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[AMR][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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7350177	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851921	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7852138	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853322	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7858373	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7859139	0.91[EUR][1000 genomes]
rs7864212	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7869419	1.00[CEU][hapmap];0.87[AMR][1000 genomes];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];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980849	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980850	0.86[AMR][1000 genomes];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
rs4742198	UHRF2	Cis_1M	lymphoblastoid	RTeQTL
rs4742198	C9orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 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	chr9:6415400-6425400	Weak transcription	Psoas Muscle	Psoas
9	chr9:6415400-6434000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:6415600-6420800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:6415600-6421000	Weak transcription	Fetal Intestine Large	intestine
12	chr9:6415600-6422000	Weak transcription	Fetal Kidney	kidney
13	chr9:6415600-6422200	Weak transcription	Lung	lung
14	chr9:6415600-6423200	Weak transcription	Stomach Mucosa	stomach
15	chr9:6415600-6430000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:6415600-6431000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
19	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr9:6416000-6420000	Weak transcription	Fetal Intestine Small	intestine
21	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:6416200-6419800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:6416400-6420600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:6416400-6421400	Weak transcription	Left Ventricle	heart
25	chr9:6416400-6421400	Weak transcription	Pancreas	Pancrea
26	chr9:6416400-6429800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:6416400-6430000	Weak transcription	Spleen	Spleen
28	chr9:6416400-6430600	Weak transcription	Right Ventricle	heart
29	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:6416600-6420000	Weak transcription	Fetal Thymus	thymus
31	chr9:6416600-6421400	Weak transcription	Fetal Muscle Leg	muscle
32	chr9:6417000-6422200	Weak transcription	Fetal Stomach	stomach
33	chr9:6417200-6422200	Weak transcription	Brain Germinal Matrix	brain
34	chr9:6417400-6420000	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr9:6417400-6420800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr9:6417400-6424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:6417400-6434400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:6417600-6421400	Weak transcription	Fetal Lung	lung
39	chr9:6417600-6430600	Weak transcription	HSMM	muscle
40	chr9:6417600-6437800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:6417800-6420000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:6417800-6420800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:6417800-6420800	Weak transcription	Liver	Liver
44	chr9:6417800-6421000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:6417800-6421200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:6417800-6422200	Weak transcription	NHLF	lung
47	chr9:6417800-6425800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr9:6417800-6426000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr9:6417800-6428600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:6417800-6428800	Weak transcription	K562	blood

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