Variant report

Variant	rs9842446
Chromosome Location	chr3:150320109-150320110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150319845-150320466	GM12878	blood:	n/a	n/a
2	RUNX3	chr3:150320071-150320392	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:150319948-150321897	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr3:150320035-150322139	GM12878	blood:	n/a	n/a
5	MTA3	chr3:150320037-150322068	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:150319975-150320582	K562	blood:	n/a	n/a
7	POLR2A	chr3:150320066-150321349	K562	blood:	n/a	n/a
8	POLR2A	chr3:150320065-150321739	K562	blood:	n/a	n/a
9	POLR2A	chr3:150320062-150322002	GM19193	blood:	n/a	n/a
10	CUX1	chr3:150319978-150320173	K562	blood:	n/a	n/a
11	POLR2A	chr3:150319798-150322130	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:150320059-150322041	GM18505	blood:	n/a	n/a
13	POLR2A	chr3:150320028-150320451	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:150320098-150320259	ProgFib	skin:	n/a	n/a
15	POLR2A	chr3:150319957-150322090	GM12891	blood:	n/a	n/a
16	MXI1	chr3:150319971-150322484	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:150319957-150320503	K562	blood:	n/a	n/a
18	WRNIP1	chr3:150319980-150322174	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:150319866-150322102	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:150319920-150322197	H1-hESC	embryonic stem cell:	n/a	n/a
21	HEY1	chr3:150320034-150320510	K562	blood:	n/a	n/a
22	POLR2A	chr3:150320081-150321943	GM12892	blood:	n/a	n/a
23	POLR2A	chr3:150319957-150320417	GM12892	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150319835..150321538-chr3:150397842..150400790,2	MCF-7	breast:
2	chr3:150260773..150268334-chr3:150317152..150324883,17	K562	blood:
3	chr3:150262222..150264859-chr3:150319269..150321349,2	K562	blood:
4	chr3:150318641..150323079-chr3:150479217..150482794,6	MCF-7	breast:
5	chr3:150319300..150322608-chr3:150420316..150423261,6	MCF-7	breast:
6	chr3:150320056..150325236-chr3:150328045..150333634,6	MCF-7	breast:
7	chr3:149955587..149957333-chr3:150319703..150322205,2	MCF-7	breast:
8	chr3:150319130..150324790-chr3:150327939..150333389,12	K562	blood:
9	chr3:150319354..150323687-chr3:150477863..150484487,11	MCF-7	breast:
10	chr3:150259884..150269236-chr3:150319275..150325391,10	MCF-7	breast:
11	chr3:150318777..150323048-chr3:150479715..150482584,4	K562	blood:
12	chr3:150320068..150322587-chr3:150419780..150423653,7	MCF-7	breast:
13	chr3:150262524..150267011-chr3:150319982..150323189,4	MCF-7	breast:
14	chr3:150319883..150326696-chr3:150327224..150333205,16	MCF-7	breast:
15	chr3:150319550..150322084-chr3:150479715..150481431,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198843	TF binding region
ENSG00000181788	Chromatin interaction
ENSG00000163645	Chromatin interaction
ENSG00000244541	Chromatin interaction
ENSG00000144895	Chromatin interaction
ENSG00000240137	Chromatin interaction
ENSG00000244265	Chromatin interaction
ENSG00000271711	Chromatin interaction
ENSG00000120742	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1133494	0.85[EUR][1000 genomes]
rs13097283	0.83[EUR][1000 genomes]
rs1915943	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2204112	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6798173	0.86[EUR][1000 genomes]
rs6801796	0.85[EUR][1000 genomes]
rs7433606	0.83[EUR][1000 genomes]
rs7638500	0.85[EUR][1000 genomes]
rs7642917	0.83[EUR][1000 genomes]
rs9809820	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9819287	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9836797	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]

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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150265600-150320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150265600-150320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:150301600-150320200	Weak transcription	Small Intestine	intestine
4	chr3:150303800-150320800	Weak transcription	Lung	lung
5	chr3:150303800-150320800	Weak transcription	Spleen	Spleen
6	chr3:150304000-150320600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:150304400-150320200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:150304400-150320600	Weak transcription	Ovary	ovary
9	chr3:150304800-150320400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:150317200-150320200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:150317200-150320200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:150317200-150320200	Weak transcription	Right Atrium	heart
13	chr3:150317400-150320200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr3:150317600-150320200	Weak transcription	HSMMtube	muscle
15	chr3:150318200-150320200	Enhancers	Primary T cells from cord blood	blood
16	chr3:150318200-150320200	Weak transcription	Right Ventricle	heart
17	chr3:150318400-150320200	Weak transcription	HSMM	muscle
18	chr3:150318600-150320200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:150318600-150320200	Weak transcription	NH-A	brain
20	chr3:150318600-150320400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:150318600-150320400	Weak transcription	NHDF-Ad	bronchial
22	chr3:150318600-150323600	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:150318600-150323600	Active TSS	K562	blood
24	chr3:150318800-150320200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:150318800-150320200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:150318800-150320200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:150318800-150320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:150318800-150320400	Weak transcription	HUVEC	blood vessel
29	chr3:150318800-150322400	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:150318800-150322400	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr3:150318800-150323600	Active TSS	GM12878-XiMat	blood
32	chr3:150319000-150320200	Weak transcription	Placenta	Placenta
33	chr3:150319000-150321200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:150319200-150320200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:150319200-150320200	Weak transcription	Fetal Lung	lung
36	chr3:150319200-150320400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:150319200-150320400	Weak transcription	Fetal Brain Male	brain
38	chr3:150319200-150320400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:150319200-150320600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:150319200-150320600	Weak transcription	Esophagus	oesophagus
41	chr3:150319200-150322800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:150319400-150323200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:150319600-150320200	Weak transcription	HepG2	liver
44	chr3:150319800-150320200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:150319800-150320200	Enhancers	Fetal Muscle Leg	muscle
46	chr3:150319800-150320400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:150319800-150320400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:150320000-150320200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr3:150320000-150320200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:150320000-150320200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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