Variant report

Variant	rs4849073
Chromosome Location	chr2:113300658-113300659
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	SREBP1	chr2:113297940-113301472	GM12878	blood:	n/a	n/a
2	GABPA	chr2:113299063-113300682	A549	lung:	n/a	n/a
3	STAT5A	chr2:113298900-113300858	GM12878	blood:	n/a	chr2:113299826-113299838 chr2:113299452-113299464 chr2:113300733-113300742 chr2:113300732-113300741 chr2:113299913-113299924
4	BRCA1	chr2:113299404-113301022	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr2:113299216-113300678	MCF-7	breast:	n/a	n/a
6	MYC	chr2:113298925-113301236	K562	blood:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
7	MAX	chr2:113299141-113300673	A549	lung:	n/a	chr2:113300065-113300075
8	MAX	chr2:113299279-113301202	Hela-S3	cervix:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
9	MAX	chr2:113299170-113301362	HepG2	liver:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
10	JUND	chr2:113298529-113301561	SK-N-SH	brain:	n/a	chr2:113299763-113299772 chr2:113299725-113299734 chr2:113300733-113300741 chr2:113300734-113300741 chr2:113300732-113300742
11	MAX	chr2:113299188-113301309	HepG2	liver:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
12	MYC	chr2:113298884-113301200	NB4	blood:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
13	CHD1	chr2:113298614-113300713	IMR90	lung:	n/a	n/a
14	MAX	chr2:113299248-113300853	ECC-1	luminal epithelium:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
15	MXI1	chr2:113298843-113301386	IMR90	lung:	n/a	n/a
16	MBD4	chr2:113299103-113301252	HepG2	liver:	n/a	n/a
17	SPI1	chr2:113300346-113300701	GM12891	blood:	n/a	n/a
18	HCFC1	chr2:113298738-113301218	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr2:113300574-113300717	K562	blood:	n/a	n/a
20	GABPA	chr2:113298734-113300671	HL-60	blood:	n/a	n/a
21	SIN3AK20	chr2:113299121-113301496	MCF-7	breast:	n/a	n/a
22	MXI1	chr2:113299297-113300844	HepG2	liver:	n/a	n/a
23	ZNF263	chr2:113299175-113301342	HEK293-T-REx	kidney:	n/a	chr2:113299454-113299463
24	POLR2A	chr2:113298841-113300948	K562	blood:	n/a	n/a
25	MYC	chr2:113299535-113301145	MCF10A-Er-Src	breast:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
26	POLR2A	chr2:113298778-113301118	GM12878	blood:	n/a	n/a
27	HCFC1	chr2:113298858-113300718	K562	blood:	n/a	n/a
28	GABPA	chr2:113299091-113300861	MCF-7	breast:	n/a	n/a
29	WRNIP1	chr2:113299002-113301076	GM12878	blood:	n/a	n/a
30	MAX	chr2:113298939-113301281	NB4	blood:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
31	MAX	chr2:113299036-113301351	HCT-116	colon:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
32	JUND	chr2:113299082-113300957	GM12878	blood:	n/a	chr2:113299763-113299772 chr2:113299725-113299734 chr2:113300733-113300741 chr2:113300734-113300741 chr2:113300732-113300742
33	MAX	chr2:113299071-113301297	A549	lung:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
34	EP300	chr2:113300522-113300677	K562	blood:	n/a	n/a
35	POLR2A	chr2:113298903-113301010	HepG2	liver:	n/a	n/a
36	MTA3	chr2:113298641-113300953	GM12878	blood:	n/a	n/a
37	MXI1	chr2:113298803-113301272	GM12878	blood:	n/a	n/a
38	KAP1	chr2:113299081-113301173	HEK293	kidney:	n/a	n/a
39	POLR2A	chr2:113298770-113301098	GM12892	blood:	n/a	n/a
40	SIN3A	chr2:113298969-113301217	H1-hESC	embryonic stem cell:	n/a	n/a
41	MXI1	chr2:113299580-113300816	K562	blood:	n/a	n/a
42	EP300	chr2:113299200-113300707	GM12878	blood:	n/a	n/a
43	NR2F2	chr2:113298891-113300785	K562	blood:	n/a	n/a
44	POLR2A	chr2:113298809-113301210	GM12891	blood:	n/a	n/a
45	SIN3AK20	chr2:113299540-113300662	A549	lung:	n/a	n/a
46	REST	chr2:113299244-113300691	HL-60	blood:	n/a	chr2:113299761-113299771
47	ELF1	chr2:113299224-113300717	MCF-7	breast:	n/a	n/a
48	JUN	chr2:113298473-113301649	K562	blood:	n/a	chr2:113299763-113299772 chr2:113299725-113299734 chr2:113300733-113300741 chr2:113300734-113300741 chr2:113300732-113300742
49	POLR2A	chr2:113298858-113301001	PFSK-1	brain:	n/a	n/a
50	MYBL2	chr2:113299086-113300885	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113300113..113302309-chr2:113304266..113305973,2	MCF-7	breast:
2	chr2:113297896..113300759-chr2:113319163..113321961,2	K562	blood:
3	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
4	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
5	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
6	chr12:52584189..52586153-chr2:113298687..113301459,2	MCF-7	breast:
7	chr2:113298665..113301106-chr2:113481233..113484131,2	MCF-7	breast:
8	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:
9	chr2:113299867..113302656-chr2:113306781..113308489,3	MCF-7	breast:
10	chr2:113032895..113034868-chr2:113298043..113301369,3	K562	blood:
11	chr17:80376042..80376941-chr2:113300332..113300909,2	Hela-S3	cervix:
12	chr2:112640408..112642506-chr2:113299856..113302341,2	K562	blood:
13	chr2:113299836..113301714-chr2:113487045..113489440,2	MCF-7	breast:
14	chr2:113298945..113301583-chr2:113309336..113312263,4	MCF-7	breast:
15	chr2:112811580..112813458-chr2:113297904..113301248,3	K562	blood:
16	chr2:113235916..113241390-chr2:113298151..113302275,12	MCF-7	breast:
17	chr2:113277911..113280966-chr2:113298764..113301565,3	MCF-7	breast:
18	chr2:112811382..112813355-chr2:113297904..113301187,3	K562	blood:
19	chr2:113012601..113015047-chr2:113298969..113301494,2	K562	blood:
20	chr2:113238238..113241697-chr2:113298157..113301092,6	K562	blood:
21	chr2:113031538..113036695-chr2:113297613..113301921,6	K562	blood:
22	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
23	chr2:113238895..113243312-chr2:113297571..113302127,8	K562	blood:
24	chr2:113235572..113240260-chr2:113300212..113305167,6	MCF-7	breast:

Variant related genes	Relation type
POLR1B	TF binding region
ENSG00000114999	Chromatin interaction
ENSG00000167767	Chromatin interaction
ENSG00000169660	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000144161	Chromatin interaction
ENSG00000181396	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10153558	0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs10153801	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10864905	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11123137	0.82[CEU][hapmap]
rs11123139	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123140	0.94[ASN][1000 genomes]
rs11123141	0.95[ASN][1000 genomes]
rs11675730	0.98[ASN][1000 genomes]
rs11676962	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11677050	0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11689338	0.94[ASN][1000 genomes]
rs11899598	0.88[CEU][hapmap]
rs12618629	0.86[ASN][1000 genomes]
rs12618882	0.96[ASN][1000 genomes]
rs13015669	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13030618	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs1437673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437675	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1545133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1595388	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17043158	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs17043167	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs2304555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35832933	0.85[ASN][1000 genomes]
rs3789723	0.96[ASN][1000 genomes]
rs3816140	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3816141	0.86[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3961775	0.98[ASN][1000 genomes]
rs3980067	0.83[ASN][1000 genomes]
rs41278940	0.99[ASN][1000 genomes]
rs41280572	0.91[ASN][1000 genomes]
rs4849072	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849074	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849075	0.96[ASN][1000 genomes]
rs4849076	0.99[ASN][1000 genomes]
rs56081241	0.90[ASN][1000 genomes]
rs60703755	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717635	0.88[CEU][hapmap]
rs7568539	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7569407	0.84[CEU][hapmap]
rs7578724	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7607358	0.92[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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4849073	TTL	cis	Skin Sun Exposed Lower leg	GTEx
rs4849073	POLR1B	cis	parietal	SCAN
rs4849073	FBLN7	cis	parietal	SCAN
rs4849073	POLR1B	cis	cerebellum	SCAN
rs4849073	LOC653596	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113298600-113301200	Active TSS	K562	blood
2	chr2:113298600-113301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:113298600-113303600	Active TSS	GM12878-XiMat	blood
4	chr2:113298800-113300800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:113298800-113300800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:113298800-113300800	Active TSS	Aorta	Aorta
7	chr2:113298800-113301200	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:113298800-113301600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:113298800-113301600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:113298800-113301600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:113299000-113300800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr2:113299000-113300800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:113299000-113300800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:113299000-113300800	Active TSS	Colonic Mucosa	Colon
15	chr2:113299000-113300800	Active TSS	Fetal Kidney	kidney
16	chr2:113299000-113300800	Active TSS	Right Atrium	heart
17	chr2:113299000-113300800	Active TSS	NHLF	lung
18	chr2:113299000-113301200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr2:113299000-113301200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:113299000-113301200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:113299000-113301600	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr2:113299000-113301600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr2:113299000-113301600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:113299000-113301600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:113299000-113301600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:113299000-113301600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr2:113299200-113300800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:113299200-113300800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:113299200-113300800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:113299200-113300800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:113299200-113300800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:113299200-113300800	Active TSS	Brain Anterior Caudate	brain
33	chr2:113299200-113300800	Active TSS	Esophagus	oesophagus
34	chr2:113299200-113300800	Active TSS	Fetal Brain Male	brain
35	chr2:113299200-113300800	Active TSS	Gastric	stomach
36	chr2:113299200-113300800	Active TSS	Left Ventricle	heart
37	chr2:113299200-113300800	Active TSS	Lung	lung
38	chr2:113299200-113300800	Active TSS	Ovary	ovary
39	chr2:113299200-113300800	Active TSS	Pancreas	Pancrea
40	chr2:113299200-113300800	Active TSS	Psoas Muscle	Psoas
41	chr2:113299200-113300800	Active TSS	Small Intestine	intestine
42	chr2:113299200-113300800	Active TSS	NHDF-Ad	bronchial
43	chr2:113299200-113301000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:113299200-113301000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:113299200-113301000	Active TSS	Fetal Intestine Small	intestine
46	chr2:113299200-113301000	Bivalent/Poised TSS	HepG2	liver
47	chr2:113299200-113301000	Active TSS	HSMMtube	muscle
48	chr2:113299200-113301200	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr2:113299200-113301200	Active TSS	Stomach Mucosa	stomach
50	chr2:113299200-113301400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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