Variant report

Variant	rs35297839
Chromosome Location	chr12:8185853-8185854
allele	A/C
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	chr12:8184725-8186282	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:8185820-8186164	H1-hESC	embryonic stem cell:	n/a	n/a
3	PML	chr12:8185833-8186101	K562	blood:	n/a	n/a
4	HCFC1	chr12:8184949-8186354	K562	blood:	n/a	n/a
5	MYC	chr12:8184925-8186264	K562	blood:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
6	MXI1	chr12:8184488-8186941	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr12:8184856-8186241	K562	blood:	n/a	n/a
8	HA-E2F1	chr12:8184850-8185910	MCF-7	breast:	n/a	chr12:8185803-8185812
9	POLR2A	chr12:8184627-8186438	K562	blood:	n/a	n/a
10	POLR2A	chr12:8185847-8186265	HCT-116	colon:	n/a	n/a
11	GTF2F1	chr12:8185644-8186186	Hela-S3	cervix:	n/a	n/a
12	HEY1	chr12:8185839-8186260	HepG2	liver:	n/a	n/a
13	MAX	chr12:8184697-8186456	A549	lung:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
14	MTA3	chr12:8184563-8186091	GM12878	blood:	n/a	n/a
15	MAZ	chr12:8184602-8186369	K562	blood:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
16	REST	chr12:8185827-8186226	K562	blood:	n/a	chr12:8185840-8185854
17	RCOR1	chr12:8185814-8186806	K562	blood:	n/a	n/a
18	POLR2A	chr12:8184794-8186414	SK-N-MC	brain:	n/a	n/a
19	TAF1	chr12:8185133-8186050	H1-neurons	neurons:	n/a	n/a
20	TAF1	chr12:8185739-8186148	K562	blood:	n/a	n/a
21	EGR1	chr12:8185826-8186297	K562	blood:	n/a	chr12:8186096-8186111 chr12:8186119-8186133 chr12:8185992-8186007
22	POLR2A	chr12:8185733-8186687	HCT-116	colon:	n/a	n/a
23	POLR2A	chr12:8185814-8186090	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr12:8185784-8186191	Hela-S3	cervix:	n/a	n/a
25	GATA1	chr12:8185763-8186408	PBDE	blood:	n/a	chr12:8186050-8186067
26	TAL1	chr12:8185842-8186377	K562	blood:	n/a	chr12:8186048-8186056 chr12:8186049-8186067
27	HEY1	chr12:8185788-8186132	K562	blood:	n/a	n/a
28	UBTF	chr12:8184512-8186288	K562	blood:	n/a	n/a
29	UBTF	chr12:8184714-8185982	K562	blood:	n/a	n/a
30	SMARCC1	chr12:8184713-8186280	Hela-S3	cervix:	n/a	n/a
31	TCF12	chr12:8184807-8186329	A549	lung:	n/a	n/a
32	REST	chr12:8184566-8186035	H1-neurons	neurons:	n/a	chr12:8185587-8185597 chr12:8185413-8185426 chr12:8185840-8185854
33	POLR2A	chr12:8184929-8186347	ProgFib	skin:	n/a	n/a
34	MAX	chr12:8184837-8185855	A549	lung:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
35	MAX	chr12:8184907-8186555	Hela-S3	cervix:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
36	MAZ	chr12:8184944-8186500	GM12878	blood:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
37	SMARCB1	chr12:8184909-8186547	Hela-S3	cervix:	n/a	chr12:8186532-8186541
38	MAX	chr12:8184830-8186007	ECC-1	luminal epithelium:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
39	TAF1	chr12:8185832-8186204	PFSK-1	brain:	n/a	n/a
40	ZBTB7A	chr12:8185421-8186194	K562	blood:	n/a	n/a
41	ZBTB7A	chr12:8185493-8185879	HepG2	liver:	n/a	n/a
42	POLR2A	chr12:8184953-8186215	K562	blood:	n/a	n/a
43	STAT5A	chr12:8185466-8185898	GM12878	blood:	n/a	n/a
44	MAZ	chr12:8184461-8186678	IMR90	lung:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
45	MXI1	chr12:8184590-8187274	IMR90	lung:	n/a	n/a
46	POLR2A	chr12:8184645-8186669	IMR90	lung:	n/a	n/a
47	SP1	chr12:8185785-8186490	H1-hESC	embryonic stem cell:	n/a	chr12:8186102-8186111 chr12:8185809-8185818 chr12:8185807-8185819 chr12:8186101-8186112 chr12:8186152-8186163 chr12:8186158-8186172 chr12:8185807-8185819 chr12:8186122-8186133 chr12:8185808-8185817 chr12:8186152-8186164
48	POLR2A	chr12:8184916-8186100	HepG2	liver:	n/a	n/a
49	MAX	chr12:8184934-8186378	GM12878	blood:	n/a	chr12:8185073-8185082 chr12:8185425-8185434
50	MAX	chr12:8184813-8186273	ECC-1	luminal epithelium:	n/a	chr12:8185073-8185082 chr12:8185425-8185434

No.	Distal block	Cell Line	Cell type
1	chr12:8183609..8186953-chr12:8232808..8236299,4	K562	blood:
2	chr12:8086985..8090687-chr12:8184864..8188373,3	K562	blood:
3	chr12:8184234..8186516-chr12:8232598..8235284,2	K562	blood:
4	chr12:8088047..8090687-chr12:8184432..8186364,2	K562	blood:

Variant related genes	Relation type
FOXJ2	TF binding region
ENSG00000089818	Chromatin interaction
ENSG00000059804	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10732571	0.81[CEU][hapmap]
rs10846366	0.80[EUR][1000 genomes]
rs7308997	0.81[CEU][hapmap]
rs7958000	0.85[CEU][hapmap]
rs7974225	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	esv1797934	chr12:7985460-8214261	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	nsv541384	chr12:8003214-8188846	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
10	nsv1040972	chr12:8003413-8266291	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
11	nsv541388	chr12:8003413-8266291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
13	esv2751118	chr12:8017473-8190206	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
14	nsv898729	chr12:8044997-8190206	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	nsv1045521	chr12:8123225-8242846	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
16	nsv898732	chr12:8123306-8190206	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
17	nsv1040958	chr12:8177050-8309724	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
18	nsv541396	chr12:8177050-8309724	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription 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	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35297839	FOXJ2	cis	parietal	SCAN
rs35297839	PRB4	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8184200-8186600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:8184400-8186000	Active TSS	Fetal Brain Female	brain
3	chr12:8184400-8186200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:8184400-8186200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:8184400-8186200	Active TSS	Rectal Smooth Muscle	rectum
6	chr12:8184400-8186600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:8184400-8187600	Active TSS	NHDF-Ad	bronchial
8	chr12:8184600-8186000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:8184600-8186000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:8184600-8186000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:8184600-8186000	Active TSS	Fetal Muscle Trunk	muscle
12	chr12:8184600-8186000	Active TSS	Psoas Muscle	Psoas
13	chr12:8184600-8186200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:8184600-8186200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:8184600-8186200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:8184600-8186400	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:8184600-8186400	Active TSS	Right Atrium	heart
18	chr12:8184600-8186600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:8184600-8186600	Active TSS	Right Ventricle	heart
20	chr12:8184600-8186800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr12:8184600-8186800	Active TSS	Left Ventricle	heart
22	chr12:8184600-8186800	Active TSS	Ovary	ovary
23	chr12:8184600-8187000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr12:8184600-8187000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:8184600-8187600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr12:8184600-8187600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:8184600-8189000	Active TSS	Aorta	Aorta
28	chr12:8184800-8186000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:8184800-8186000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:8184800-8186000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:8184800-8186000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:8184800-8186000	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr12:8184800-8186000	Active TSS	Brain Substantia Nigra	brain
34	chr12:8184800-8186000	Active TSS	Duodenum Mucosa	Duodenum
35	chr12:8184800-8186000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr12:8184800-8186000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr12:8184800-8186000	Active TSS	Fetal Intestine Small	intestine
38	chr12:8184800-8186000	Active TSS	Fetal Muscle Leg	muscle
39	chr12:8184800-8186000	Active TSS	Lung	lung
40	chr12:8184800-8186000	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr12:8184800-8186000	Active TSS	HMEC	breast
42	chr12:8184800-8186000	Active TSS	HSMM	muscle
43	chr12:8184800-8186000	Active TSS	HSMMtube	muscle
44	chr12:8184800-8186200	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr12:8184800-8186200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:8184800-8186200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr12:8184800-8186200	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr12:8184800-8186200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:8184800-8186200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:8184800-8186200	Active TSS	Primary T cells from cord blood	blood

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