Variant report

Variant	rs35514263
Chromosome Location	chr3:142298044-142298045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:303)
CpG islands
(count:61)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:303 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr3:142297144-142298130	MCF-7	breast:	n/a	chr3:142297742-142297751
2	MAX	chr3:142296519-142298266	A549	lung:	n/a	n/a
3	POLR2A	chr3:142297255-142298092	HUVEC	blood vessel:	n/a	n/a
4	TAF7	chr3:142297111-142298183	H1-hESC	embryonic stem cell:	n/a	n/a
5	RFX5	chr3:142297425-142298050	GM12878	blood:	n/a	n/a
6	SIN3AK20	chr3:142296938-142298318	MCF-7	breast:	n/a	n/a
7	HCFC1	chr3:142297271-142298052	K562	blood:	n/a	n/a
8	MTA3	chr3:142296982-142298737	GM12878	blood:	n/a	n/a
9	ELF1	chr3:142297161-142298080	K562	blood:	n/a	chr3:142297609-142297622 chr3:142297661-142297670
10	MYC	chr3:142297015-142298118	K562	blood:	n/a	n/a
11	TAF1	chr3:142297254-142298084	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:142297104-142298113	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:142297198-142298185	ProgFib	skin:	n/a	n/a
14	EGR1	chr3:142297190-142298141	HCT-116	colon:	n/a	chr3:142297742-142297752
15	POLR2A	chr3:142297104-142298105	K562	blood:	n/a	n/a
16	ELF1	chr3:142297158-142298229	SK-N-SH	brain:	n/a	chr3:142297609-142297622 chr3:142297661-142297670
17	MXI1	chr3:142297007-142298484	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:142297265-142298328	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:142296959-142298595	GM18505	blood:	n/a	n/a
20	BCL3	chr3:142297172-142298106	A549	lung:	n/a	chr3:142297368-142297381
21	PBX3	chr3:142297297-142298083	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr3:142297483-142298187	K562	blood:	n/a	n/a
23	MAZ	chr3:142297163-142298074	K562	blood:	n/a	n/a
24	MXI1	chr3:142296835-142298116	HepG2	liver:	n/a	n/a
25	MAX	chr3:142297134-142298137	SK-N-SH	brain:	n/a	n/a
26	NFIC	chr3:142296728-142298205	GM12878	blood:	n/a	n/a
27	GABPA	chr3:142296978-142298093	MCF-7	breast:	n/a	chr3:142297742-142297751
28	POLR2A	chr3:142296973-142298242	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:142297399-142298051	HepG2	liver:	n/a	n/a
30	REST	chr3:142296787-142298145	H1-neurons	neurons:	n/a	n/a
31	SIN3AK20	chr3:142297003-142298074	SK-N-SH	brain:	n/a	n/a
32	CREB1	chr3:142297278-142298072	H1-hESC	embryonic stem cell:	n/a	n/a
33	MXI1	chr3:142296712-142298139	Hela-S3	cervix:	n/a	n/a
34	YY1	chr3:142297222-142298095	GM12878	blood:	n/a	chr3:142297370-142297381 chr3:142297742-142297751
35	SP1	chr3:142297068-142298154	A549	lung:	n/a	chr3:142297742-142297751 chr3:142297742-142297752 chr3:142297743-142297752 chr3:142297738-142297752 chr3:142297741-142297753 chr3:142297741-142297753 chr3:142297410-142297419 chr3:142297742-142297752 chr3:142297743-142297752
36	ELK4	chr3:142297120-142298062	Hela-S3	cervix:	n/a	chr3:142297612-142297623 chr3:142297661-142297672
37	POLR2A	chr3:142297125-142298432	GM18951	blood:	n/a	n/a
38	POLR2A	chr3:142297222-142298126	ECC-1	luminal epithelium:	n/a	n/a
39	ELK1	chr3:142297412-142298110	GM12878	blood:	n/a	n/a
40	SIN3AK20	chr3:142296994-142298224	HCT-116	colon:	n/a	n/a
41	SP1	chr3:142297166-142298260	A549	lung:	n/a	chr3:142297742-142297751 chr3:142297742-142297752 chr3:142297743-142297752 chr3:142297738-142297752 chr3:142297741-142297753 chr3:142297741-142297753 chr3:142297410-142297419 chr3:142297742-142297752 chr3:142297743-142297752
42	CREB1	chr3:142296840-142298154	GM12878	blood:	n/a	n/a
43	TCF7L2	chr3:142296953-142298068	PANC-1	pancreas:	n/a	chr3:142296959-142296968 chr3:142296956-142296972
44	SMC3	chr3:142297467-142298098	Hela-S3	cervix:	n/a	n/a
45	CREB1	chr3:142297338-142298082	HepG2	liver:	n/a	n/a
46	ELK1	chr3:142297511-142298066	K562	blood:	n/a	n/a
47	POLR2A	chr3:142297140-142298173	K562	blood:	n/a	n/a
48	POLR2A	chr3:142297167-142298103	K562	blood:	n/a	n/a
49	POLR2A	chr3:142297197-142298123	HUVEC	blood vessel:	n/a	n/a
50	YY1	chr3:142297123-142298081	GM12878	blood:	n/a	chr3:142297370-142297381 chr3:142297742-142297751

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142298018-142298068	HepG2	liver:	n/a
2	chr3:142298018-142298068	Caco-2	colon:	n/a
3	chr3:142298018-142298068	BJ	skin:	n/a
4	chr3:142298018-142298068	IMR90	lung:	fetal
5	chr3:142298018-142298068	RPTEC	kidney:	n/a
6	chr3:142298018-142298068	NH-A	brain:	n/a
7	chr3:142298018-142298068	SK-N-SH_RA	brain:	n/a
8	chr3:142298018-142298068	SK-N-SH	brain:	n/a
9	chr3:142298018-142298068	AG10803	skin:	n/a
10	chr3:142298018-142298068	GM12878	blood:	n/a
11	chr3:142298018-142298068	HRCEpiC	kidney:	n/a
12	chr3:142298018-142298068	NHDF-neo	bronchial:	n/a
13	chr3:142298018-142298068	Hepatocyte	liver:	n/a
14	chr3:142298018-142298068	CMK	blood:	n/a
15	chr3:142298018-142298068	U87	brain:	n/a
16	chr3:142298018-142298068	NT2-D1	testis:	n/a
17	chr3:142298018-142298068	AG09319	gingival:	n/a
18	chr3:142298018-142298068	AG04449	skin:	fetal
19	chr3:142298018-142298068	BE2_C	brain:	n/a
20	chr3:142298018-142298068	GM19239	blood:	n/a
21	chr3:142298018-142298068	HCF	heart:	n/a
22	chr3:142298018-142298068	HAEpiC	amniotic membrane:	n/a
23	chr3:142298018-142298068	SAEC	small airway:	n/a
24	chr3:142298018-142298068	GM06990	blood:	n/a
25	chr3:142298018-142298068	K562	blood:	n/a
26	chr3:142298018-142298068	GM12891	blood:	n/a
27	chr3:142298018-142298068	T-47D	breast:	n/a
28	chr3:142298018-142298068	HRPEpiC	eye:	n/a
29	chr3:142298018-142298068	LNCaP	prostate:	n/a
30	chr3:142298018-142298068	PrEC	prostate:	n/a
31	chr3:142298018-142298068	HRE	kidney:	n/a
32	chr3:142298018-142298068	HCPEpiC	choroid plexus:	n/a
33	chr3:142298018-142298068	HMEC	breast:	n/a
34	chr3:142298018-142298068	GM12892	blood:	n/a
35	chr3:142298018-142298068	HIPEpiC	eye:	n/a
36	chr3:142298018-142298068	HEK293	kidney:	embryo
37	chr3:142298018-142298068	ovcar-3	ovarian:	n/a
38	chr3:142298018-142298068	SKMC	muscle:	n/a
39	chr3:142298018-142298068	AoSMC	blood vessel:	n/a
40	chr3:142298018-142298068	HCT-116	colon:	n/a
41	chr3:142298018-142298068	Jurkat	blood:	n/a
42	chr3:142298018-142298068	H1-hESC	embryonic stem cell:	embryo
43	chr3:142298018-142298068	HPAEpiC	pulmonary alveolar:	n/a
44	chr3:142298018-142298068	Hela-S3	cervix:	n/a
45	chr3:142298018-142298068	PANC-1	pancreas:	n/a
46	chr3:142298018-142298068	MCF10A-Er-Src	breast:	n/a
47	chr3:142298018-142298068	ECC-1	luminal epithelium:	n/a
48	chr3:142298018-142298068	A549	lung:	n/a
49	chr3:142298018-142298068	SK-N-MC	brain:	n/a
50	chr3:142298018-142298068	ProgFib	skin:	n/a

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142297806..142298379-chr5:1524091..1524637,2	NB4	blood:
2	chr3:142297625..142299268-chr3:142441632..142444151,3	K562	blood:
3	chr3:142280626..142282527-chr3:142296623..142299039,2	K562	blood:
4	chr12:46753334..46754030-chr3:142297866..142298600,2	Hela-S3	cervix:
5	chr3:142297403..142299294-chr3:142720282..142722143,3	MCF-7	breast:
6	chr3:142296149..142300233-chr3:142313670..142315817,6	K562	blood:
7	chr3:142297196..142298101-chr5:71615499..71616255,2	Hela-S3	cervix:
8	chr3:142297466..142299799-chr3:142313558..142315620,3	K562	blood:
9	chr3:142295918..142298932-chr3:142719049..142722504,4	MCF-7	breast:
10	chr3:142280626..142283157-chr3:142296079..142299039,3	K562	blood:
11	chr3:142297625..142299268-chr3:142441632..142445353,4	K562	blood:
12	chr13:98628143..98628846-chr3:142297511..142298310,2	NB4	blood:
13	chr3:142217843..142219879-chr3:142296547..142298953,2	MCF-7	breast:
14	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
15	chr3:142296202..142300183-chr3:142719946..142722583,4	K562	blood:
16	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
17	chr3:142295888..142299099-chr3:142720440..142723490,3	K562	blood:
18	chr3:142297949..142299634-chr3:142710792..142712643,2	MCF-7	breast:
19	chr17:27046573..27047488-chr3:142297296..142298228,2	Hela-S3	cervix:
20	chr3:142296891..142299259-chr3:142680803..142682548,2	K562	blood:

No data

Variant related genes	Relation type
ATR	TF binding region
RPL6P9	TF binding region
ATR	CpG island
RPL6P9	CpG island
ENSG00000049883	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000065150	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000188582	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000153395	Chromatin interaction
ENSG00000113048	Chromatin interaction
ENSG00000198242	Chromatin interaction
ENSG00000241570	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12629684	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12635122	0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6796656	1.00[YRI][hapmap]
rs7644719	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic 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	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 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	chr3:142293800-142298400	Active TSS	GM12878-XiMat	blood
2	chr3:142296000-142298400	Active TSS	K562	blood
3	chr3:142296200-142298200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:142296200-142298200	Active TSS	NHLF	lung
5	chr3:142296200-142298400	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:142296200-142298400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:142296200-142298400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:142296200-142298400	Active TSS	Psoas Muscle	Psoas
9	chr3:142296200-142298400	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:142296200-142298600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:142296400-142298200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:142296400-142298200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:142296400-142298200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:142296400-142298200	Active TSS	Left Ventricle	heart
15	chr3:142296400-142298200	Active TSS	A549	lung
16	chr3:142296400-142298400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr3:142296400-142298400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:142296400-142298400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:142296400-142298400	Active TSS	Colonic Mucosa	Colon
20	chr3:142296400-142298400	Active TSS	Fetal Intestine Large	intestine
21	chr3:142296400-142298400	Active TSS	Right Ventricle	heart
22	chr3:142296400-142298400	Active TSS	HSMMtube	muscle
23	chr3:142296400-142298400	Active TSS	NHDF-Ad	bronchial
24	chr3:142296400-142298600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:142296600-142298200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:142296600-142298200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:142296600-142298200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:142296600-142298200	Active TSS	Aorta	Aorta
29	chr3:142296600-142298200	Active TSS	Esophagus	oesophagus
30	chr3:142296600-142298200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr3:142296600-142298200	Active TSS	Ovary	ovary
32	chr3:142296600-142298200	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr3:142296600-142298400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr3:142296600-142298400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:142296600-142298400	Active TSS	Fetal Muscle Trunk	muscle
36	chr3:142296600-142298600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr3:142296600-142298600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr3:142296800-142298200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:142296800-142298200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:142296800-142298200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:142296800-142298200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:142296800-142298200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:142296800-142298200	Active TSS	Fetal Intestine Small	intestine
44	chr3:142296800-142298200	Active TSS	Fetal Kidney	kidney
45	chr3:142296800-142298200	Active TSS	Lung	lung
46	chr3:142296800-142298200	Active TSS	Pancreas	Pancrea
47	chr3:142296800-142298200	Active TSS	Placenta Amnion	Placenta Amnion
48	chr3:142296800-142298200	Active TSS	Dnd41	blood
49	chr3:142296800-142298200	Bivalent/Poised TSS	HepG2	liver
50	chr3:142296800-142298200	Active TSS	NH-A	brain

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