Variant report

Variant	rs12535954
Chromosome Location	chr7:7609106-7609107
allele	C/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	TBP	chr7:7607313-7609708	GM12878	blood:	n/a	n/a
2	MXI1	chr7:7606284-7609622	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:7606180-7609855	GM12892	blood:	n/a	n/a
4	FOXM1	chr7:7608528-7609113	GM12878	blood:	n/a	n/a
5	EP300	chr7:7608505-7609249	GM12878	blood:	n/a	chr7:7608822-7608836
6	NFATC1	chr7:7608450-7609311	GM12878	blood:	n/a	n/a
7	TBL1XR1	chr7:7608295-7609722	GM12878	blood:	n/a	n/a
8	MEF2A	chr7:7608537-7609166	GM12878	blood:	n/a	chr7:7608707-7608722
9	ATF2	chr7:7608247-7609672	GM12878	blood:	n/a	n/a
10	CREB1	chr7:7608511-7609106	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:7608989-7609108	Hela-S3	cervix:	n/a	n/a
12	ZNF384	chr7:7608104-7609118	GM12878	blood:	n/a	n/a
13	POLR2A	chr7:7607548-7610838	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:7607549-7609826	GM12892	blood:	n/a	n/a
15	BCLAF1	chr7:7608244-7609192	GM12878	blood:	n/a	n/a
16	ZNF143	chr7:7608625-7609569	GM12878	blood:	n/a	n/a
17	CHD1	chr7:7608203-7609706	GM12878	blood:	n/a	n/a
18	ELF1	chr7:7608707-7609124	GM12878	blood:	n/a	n/a
19	PML	chr7:7608278-7609709	GM12878	blood:	n/a	n/a
20	NFIC	chr7:7608505-7609146	GM12878	blood:	n/a	n/a
21	ELK1	chr7:7608622-7609582	GM12878	blood:	n/a	n/a
22	CHD2	chr7:7608613-7609584	GM12878	blood:	n/a	n/a
23	POLR2A	chr7:7606226-7609771	GM12892	blood:	n/a	n/a
24	SPI1	chr7:7608362-7609214	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:7608572-7609721	GM12891	blood:	n/a	n/a
26	ATF2	chr7:7608458-7609151	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:7606063-7609760	GM19099	blood:	n/a	n/a
28	POLR2A	chr7:7608142-7609744	GM12892	blood:	n/a	n/a
29	POU2F2	chr7:7608598-7609751	GM12878	blood:	n/a	n/a
30	MEF2A	chr7:7608565-7609149	GM12878	blood:	n/a	chr7:7608707-7608722
31	POLR2A	chr7:7608745-7609209	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr7:7606056-7610648	GM12891	blood:	n/a	n/a
33	NFATC1	chr7:7608506-7610011	GM12878	blood:	n/a	n/a
34	POLR2A	chr7:7606087-7610683	GM12892	blood:	n/a	n/a
35	POLR2A	chr7:7608503-7609682	GM12891	blood:	n/a	n/a
36	RCOR1	chr7:7607566-7609706	GM12878	blood:	n/a	n/a
37	POLR2A	chr7:7607888-7609742	GM12878	blood:	n/a	n/a
38	POLR2A	chr7:7606006-7610933	GM12878	blood:	n/a	n/a
39	BHLHE40	chr7:7608593-7609315	GM12878	blood:	n/a	n/a
40	POLR2A	chr7:7606174-7610054	GM18505	blood:	n/a	n/a
41	POLR2A	chr7:7606127-7610748	GM12878	blood:	n/a	n/a
42	CREB1	chr7:7608516-7609411	GM12878	blood:	n/a	n/a
43	WRNIP1	chr7:7608710-7609720	GM12878	blood:	n/a	n/a
44	MTA3	chr7:7606085-7609611	GM12878	blood:	n/a	n/a
45	MAX	chr7:7608708-7609637	GM12878	blood:	n/a	n/a
46	MAZ	chr7:7608447-7609297	GM12878	blood:	n/a	n/a
47	POLR2A	chr7:7608534-7609665	GM12891	blood:	n/a	n/a
48	NFIC	chr7:7608455-7609120	GM12878	blood:	n/a	n/a
49	POLR2A	chr7:7608581-7609688	GM12891	blood:	n/a	n/a
50	POLR2A	chr7:7606253-7610047	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7605291..7607922-chr7:7608027..7610593,4	MCF-7	breast:
2	chr7:7588099..7594648-chr7:7604621..7611487,9	MCF-7	breast:
3	chr7:7608142..7610362-chr7:7619716..7621780,2	K562	blood:
4	chr7:7605958..7609334-chr7:7621457..7626452,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272894	TF binding region
ENSG00000272894	Chromatin interaction
ENSG00000164654	Chromatin interaction
ENSG00000272732	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10085718	1.00[ASN][1000 genomes]
rs1013002	0.91[EUR][1000 genomes]
rs1016028	0.86[EUR][1000 genomes]
rs11976831	0.86[EUR][1000 genomes]
rs11983756	0.82[EUR][1000 genomes]
rs17167617	1.00[ASN][1000 genomes]
rs2051910	0.82[EUR][1000 genomes]
rs2051912	0.82[EUR][1000 genomes]
rs2051913	0.82[EUR][1000 genomes]
rs2051914	0.82[EUR][1000 genomes]
rs2108067	0.86[EUR][1000 genomes]
rs2190248	0.86[EUR][1000 genomes]
rs2348047	1.00[ASN][1000 genomes]
rs2348265	0.82[EUR][1000 genomes]
rs2348339	0.91[EUR][1000 genomes]
rs28847278	1.00[ASN][1000 genomes]
rs4380838	0.82[EUR][1000 genomes]
rs4720741	0.91[EUR][1000 genomes]
rs6463702	1.00[ASN][1000 genomes]
rs6463705	0.82[EUR][1000 genomes]
rs6946022	0.91[EUR][1000 genomes]
rs6946425	0.82[EUR][1000 genomes]
rs6948157	0.86[EUR][1000 genomes]
rs6962939	1.00[ASN][1000 genomes]
rs6964397	0.86[EUR][1000 genomes]
rs6974246	0.82[EUR][1000 genomes]
rs73346346	1.00[ASN][1000 genomes]
rs73347196	1.00[ASN][1000 genomes]
rs73347201	1.00[ASN][1000 genomes]
rs73348905	1.00[ASN][1000 genomes]
rs7783239	0.82[EUR][1000 genomes]
rs7789187	0.86[EUR][1000 genomes]
rs7789287	0.82[EUR][1000 genomes]
rs7791344	0.91[EUR][1000 genomes]
rs7796709	0.86[EUR][1000 genomes]
rs7801367	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7805565	0.82[EUR][1000 genomes]
rs7806046	0.82[EUR][1000 genomes]
rs7808788	0.86[EUR][1000 genomes]
rs7810367	0.82[EUR][1000 genomes]
rs9640043	0.86[EUR][1000 genomes]
rs9640044	0.82[EUR][1000 genomes]
rs9640045	0.82[EUR][1000 genomes]
rs972600	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
12	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7606000-7609200	Active TSS	Right Atrium	heart
2	chr7:7606200-7609800	Active TSS	GM12878-XiMat	blood
3	chr7:7607000-7609400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr7:7607200-7609200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr7:7607200-7609200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:7607200-7609200	Weak transcription	Spleen	Spleen
7	chr7:7607200-7609400	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr7:7607200-7609600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr7:7607200-7609800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr7:7607200-7648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:7607400-7609200	Weak transcription	Gastric	stomach
12	chr7:7607400-7609400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:7607400-7609400	Enhancers	Small Intestine	intestine
14	chr7:7607400-7609600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr7:7607400-7610200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:7607400-7612400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
17	chr7:7607400-7646400	Weak transcription	Esophagus	oesophagus
18	chr7:7607400-7648200	Weak transcription	Lung	lung
19	chr7:7607600-7609200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr7:7607600-7610600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:7607600-7610600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr7:7607600-7612000	Weak transcription	Ovary	ovary
23	chr7:7607600-7612200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:7607600-7613400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr7:7607600-7646400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:7607600-7648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:7607800-7609200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
28	chr7:7607800-7621400	Weak transcription	Aorta	Aorta
29	chr7:7608000-7609200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:7608000-7609400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:7608000-7609400	Enhancers	Brain Cingulate Gyrus	brain
32	chr7:7608000-7609400	Enhancers	Stomach Mucosa	stomach
33	chr7:7608000-7609600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr7:7608000-7609600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:7608000-7609600	Enhancers	Adipose Nuclei	Adipose
36	chr7:7608000-7609600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr7:7608000-7610600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr7:7608000-7612800	Weak transcription	HSMMtube	muscle
39	chr7:7608200-7609400	Enhancers	Brain Substantia Nigra	brain
40	chr7:7608200-7609400	Enhancers	Fetal Heart	heart
41	chr7:7608200-7609600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:7608200-7609600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:7608200-7612200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr7:7608200-7612400	Weak transcription	Fetal Intestine Large	intestine
45	chr7:7608200-7648800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr7:7608400-7609200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr7:7608400-7609200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:7608400-7609200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr7:7608400-7609200	Enhancers	Brain Anterior Caudate	brain
50	chr7:7608400-7609200	Weak transcription	Left Ventricle	heart

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