Variant report

Variant	rs2240450
Chromosome Location	chr7:108209119-108209120
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	POLR2A	chr7:108209074-108209405	HCT-116	colon:	n/a	n/a
2	POLR2A	chr7:108209066-108211445	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:108208976-108212142	MCF10A-Er-Src	breast:	n/a	n/a
4	JUN	chr7:108208251-108211889	K562	blood:	n/a	n/a
5	POLR2A	chr7:108208967-108210802	SK-N-MC	brain:	n/a	n/a
6	HCFC1	chr7:108209080-108211919	Hela-S3	cervix:	n/a	n/a
7	CBX3	chr7:108209070-108211254	K562	blood:	n/a	n/a
8	CUX1	chr7:108209116-108210638	K562	blood:	n/a	n/a
9	BHLHE40	chr7:108208641-108211651	K562	blood:	n/a	chr7:108209635-108209648
10	BHLHE40	chr7:108209010-108211311	GM12878	blood:	n/a	chr7:108209635-108209648
11	POLR2A	chr7:108209032-108211612	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr7:108199426-108221976	K562	blood:	n/a	n/a
13	POLR2A	chr7:108209105-108210734	GM12891	blood:	n/a	n/a
14	POLR2A	chr7:108208528-108211292	K562	blood:	n/a	n/a
15	POLR2A	chr7:108209049-108210734	HUVEC	blood vessel:	n/a	n/a
16	TEAD4	chr7:108208975-108211406	K562	blood:	n/a	n/a
17	POLR2A	chr7:108208993-108211456	IMR90	lung:	n/a	n/a
18	IRF1	chr7:108208152-108210573	K562	blood:	n/a	chr7:108209590-108209602 chr7:108208528-108208541 chr7:108208531-108208542 chr7:108208530-108208544
19	STAT3	chr7:108209115-108210379	GM12878	blood:	n/a	chr7:108210127-108210138 chr7:108209345-108209352
20	POLR2A	chr7:108209111-108210741	GM12892	blood:	n/a	n/a
21	MTA3	chr7:108209080-108211349	GM12878	blood:	n/a	n/a
22	MXI1	chr7:108207302-108212533	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr7:108208955-108211322	K562	blood:	n/a	n/a
24	POLR2A	chr7:108208325-108211370	K562	blood:	n/a	n/a
25	POLR2A	chr7:108209111-108211595	GM12878	blood:	n/a	n/a
26	POLR2A	chr7:108208446-108211787	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr7:108209104-108211297	GM12892	blood:	n/a	n/a
28	POLR2A	chr7:108209087-108211746	GM18505	blood:	n/a	n/a
29	IRF1	chr7:108208908-108212102	K562	blood:	n/a	chr7:108212006-108212020 chr7:108211827-108211841 chr7:108209590-108209602 chr7:108212010-108212020 chr7:108212003-108212015 chr7:108212010-108212024
30	POLR2A	chr7:108209003-108211248	GM19099	blood:	n/a	n/a
31	JUN	chr7:108208875-108209273	K562	blood:	n/a	n/a
32	ARID3A	chr7:108208922-108210357	K562	blood:	n/a	n/a
33	POLR2A	chr7:108209039-108211508	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:108164038..108167949-chr7:108208349..108211666,8	MCF-7	breast:
2	chr7:107383523..107385849-chr7:108208781..108210517,2	K562	blood:
3	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:
4	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
5	chr7:108208069..108211100-chr7:112089167..112092388,3	K562	blood:
6	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:

Variant related genes	Relation type
DNAJB9	TF binding region
ENSG00000006652	Chromatin interaction
ENSG00000105879	Chromatin interaction
ENSG00000241764	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10239916	1.00[GIH][hapmap]
rs10241941	1.00[GIH][hapmap]
rs10264851	1.00[GIH][hapmap]
rs10280579	1.00[GIH][hapmap]
rs10452962	1.00[MEX][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs17155959	1.00[MEX][hapmap];0.90[YRI][hapmap]
rs2286259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395996	1.00[GIH][hapmap]
rs2395997	1.00[GIH][hapmap]
rs2395999	1.00[GIH][hapmap]
rs4730310	1.00[GIH][hapmap]
rs55657836	0.81[AFR][1000 genomes]
rs55687634	0.81[AFR][1000 genomes]
rs56010627	0.81[AFR][1000 genomes]
rs56262432	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60598865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466227	1.00[GIH][hapmap]
rs6466228	1.00[GIH][hapmap]
rs6466229	1.00[GIH][hapmap]
rs6945432	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6955463	0.81[AFR][1000 genomes]
rs6977190	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73426137	0.90[ASN][1000 genomes]
rs73713149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73713163	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73713171	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788503	1.00[GIH][hapmap]
rs7802157	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108200400-108209400	Weak transcription	Spleen	Spleen
2	chr7:108202200-108209200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:108205200-108209400	Weak transcription	Gastric	stomach
4	chr7:108205400-108209200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:108206400-108209200	Weak transcription	Aorta	Aorta
6	chr7:108206400-108209200	Weak transcription	Fetal Muscle Leg	muscle
7	chr7:108206400-108209200	Weak transcription	Ovary	ovary
8	chr7:108207000-108209200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:108207000-108209200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr7:108207200-108209200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:108207200-108209200	Enhancers	Fetal Heart	heart
12	chr7:108207400-108213400	Active TSS	GM12878-XiMat	blood
13	chr7:108207600-108212000	Active TSS	K562	blood
14	chr7:108207800-108209600	Flanking Active TSS	Dnd41	blood
15	chr7:108208200-108209200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:108208200-108209600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr7:108208400-108209200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr7:108208400-108209200	Enhancers	Primary B cells from peripheral blood	blood
19	chr7:108208400-108209200	Enhancers	Primary hematopoietic stem cells	blood
20	chr7:108208400-108209200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:108208400-108209200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:108208400-108209200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr7:108208400-108209200	Enhancers	Fetal Intestine Small	intestine
24	chr7:108208400-108209200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr7:108208400-108209200	Enhancers	Rectal Smooth Muscle	rectum
26	chr7:108208400-108209200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr7:108208400-108209400	Enhancers	Small Intestine	intestine
28	chr7:108208400-108209400	Enhancers	Stomach Mucosa	stomach
29	chr7:108208400-108209600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:108208400-108209600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr7:108208400-108209600	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr7:108208400-108209600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr7:108208400-108209600	Flanking Active TSS	Hela-S3	cervix
34	chr7:108208400-108209800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr7:108208400-108209800	Active TSS	Stomach Smooth Muscle	stomach
36	chr7:108208400-108211400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:108208400-108211800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:108208400-108212000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr7:108208600-108209200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:108208600-108209200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr7:108208600-108209200	Enhancers	Adipose Nuclei	Adipose
42	chr7:108208600-108209200	Enhancers	Colonic Mucosa	Colon
43	chr7:108208600-108209200	Enhancers	Fetal Intestine Large	intestine
44	chr7:108208600-108209200	Enhancers	Fetal Muscle Trunk	muscle
45	chr7:108208600-108209200	Enhancers	Left Ventricle	heart
46	chr7:108208600-108209200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr7:108208600-108209200	Enhancers	Thymus	Thymus
48	chr7:108208600-108209400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:108208600-108209400	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr7:108208600-108209600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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