Variant report

Variant	rs4849074
Chromosome Location	chr2:113301237-113301238
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	MAX	chr2:113299170-113301362	HepG2	liver:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
3	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
4	MAX	chr2:113299188-113301309	HepG2	liver:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
5	MXI1	chr2:113298843-113301386	IMR90	lung:	n/a	n/a
6	MAX	chr2:113300875-113301295	H1-hESC	embryonic stem cell:	n/a	n/a
7	MBD4	chr2:113299103-113301252	HepG2	liver:	n/a	n/a
8	SIN3AK20	chr2:113299121-113301496	MCF-7	breast:	n/a	n/a
9	ZNF263	chr2:113299175-113301342	HEK293-T-REx	kidney:	n/a	chr2:113299454-113299463
10	GATA2	chr2:113300869-113301283	SH-SY5Y	brain:	n/a	chr2:113301189-113301197
11	RCOR1	chr2:113300832-113301338	K562	blood:	n/a	n/a
12	MAX	chr2:113298939-113301281	NB4	blood:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
13	MAX	chr2:113299036-113301351	HCT-116	colon:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
14	MAX	chr2:113299071-113301297	A549	lung:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
15	MXI1	chr2:113298803-113301272	GM12878	blood:	n/a	n/a
16	CTCF	chr2:113301100-113301250	A549	lung:	n/a	n/a
17	JUN	chr2:113298473-113301649	K562	blood:	n/a	chr2:113299763-113299772 chr2:113299725-113299734 chr2:113300733-113300741 chr2:113300734-113300741 chr2:113300732-113300742
18	MAX	chr2:113299160-113301291	HCT-116	colon:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
19	MYC	chr2:113298943-113301291	K562	blood:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075
20	MXI1	chr2:113298346-113301743	SK-N-SH	brain:	n/a	n/a
21	RUNX3	chr2:113300889-113301323	GM12878	blood:	n/a	n/a
22	MYC	chr2:113299700-113301237	MCF10A-Er-Src	breast:	n/a	chr2:113300733-113300742 chr2:113300732-113300741 chr2:113300065-113300075

No.	Distal block	Cell Line	Cell type
1	chr2:113300113..113302309-chr2:113304266..113305973,2	MCF-7	breast:
2	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
3	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
4	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
5	chr12:52584189..52586153-chr2:113298687..113301459,2	MCF-7	breast:
6	chr2:113297047..113302352-chr2:113483159..113487384,5	K562	blood:
7	chr2:113299867..113302656-chr2:113306781..113308489,3	MCF-7	breast:
8	chr2:113032895..113034868-chr2:113298043..113301369,3	K562	blood:
9	chr2:112640408..112642506-chr2:113299856..113302341,2	K562	blood:
10	chr2:113299836..113301714-chr2:113487045..113489440,2	MCF-7	breast:
11	chr2:113298945..113301583-chr2:113309336..113312263,4	MCF-7	breast:
12	chr2:112811580..112813458-chr2:113297904..113301248,3	K562	blood:
13	chr2:113235916..113241390-chr2:113298151..113302275,12	MCF-7	breast:
14	chr2:113277911..113280966-chr2:113298764..113301565,3	MCF-7	breast:
15	chr2:113012601..113015047-chr2:113298969..113301494,2	K562	blood:
16	chr2:113031538..113036695-chr2:113297613..113301921,6	K562	blood:
17	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
18	chr2:113238895..113243312-chr2:113297571..113302127,8	K562	blood:
19	chr2:113300762..113301271-chr8:120350227..120350748,2	MCF-7	breast:
20	chr2:113235572..113240260-chr2:113300212..113305167,6	MCF-7	breast:

Variant related genes	Relation type
POLR1B	TF binding region
ENSG00000144161	Chromatin interaction
ENSG00000167767	Chromatin interaction
ENSG00000153107	Chromatin interaction
ENSG00000125611	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000153214	Chromatin interaction
ENSG00000144130	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];0.82[ASN][1000 genomes]
rs10153801	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10864905	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11123137	0.82[CEU][hapmap]
rs11123139	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123140	0.93[ASN][1000 genomes]
rs11123141	0.95[ASN][1000 genomes]
rs11675730	0.98[ASN][1000 genomes]
rs11676962	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11677050	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11689338	0.93[ASN][1000 genomes]
rs11899598	0.88[CEU][hapmap]
rs12618629	0.85[ASN][1000 genomes]
rs12618882	0.96[ASN][1000 genomes]
rs13015669	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13030618	0.84[CEU][hapmap]
rs1437673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1437675	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1545133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1595388	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17043158	0.88[CEU][hapmap]
rs17043167	0.88[CEU][hapmap]
rs2304555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs35832933	0.84[ASN][1000 genomes]
rs3789723	0.95[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];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3961775	0.98[ASN][1000 genomes]
rs3980067	0.81[ASN][1000 genomes]
rs41278940	0.98[ASN][1000 genomes]
rs41280572	0.91[ASN][1000 genomes]
rs4849072	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849073	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	0.98[ASN][1000 genomes]
rs56081241	0.89[ASN][1000 genomes]
rs60703755	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6717635	0.88[CEU][hapmap]
rs7568539	0.95[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];0.88[ASN][1000 genomes]
rs7607358	0.91[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
rs4849074	POLR1B	cis	parietal	SCAN
rs4849074	TTL	cis	Skin Sun Exposed Lower leg	GTEx
rs4849074	FBLN7	cis	parietal	SCAN
rs4849074	LOC653596	cis	multi-tissue	Pritchard
rs4849074	POLR1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113298600-113301600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:113298600-113303600	Active TSS	GM12878-XiMat	blood
3	chr2:113298800-113301600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:113298800-113301600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:113298800-113301600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:113299000-113301600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:113299000-113301600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr2:113299000-113301600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:113299000-113301600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:113299000-113301600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr2:113299000-113301600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr2:113299200-113301400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:113299200-113301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:113299200-113301400	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr2:113299200-113301600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:113299200-113301600	Active TSS	A549	lung
17	chr2:113299200-113301600	Active TSS	HSMM	muscle
18	chr2:113299400-113301400	Active TSS	Fetal Intestine Large	intestine
19	chr2:113299400-113302400	Active TSS	Hela-S3	cervix
20	chr2:113300000-113301400	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr2:113300000-113301400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:113300000-113301600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:113300000-113301600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr2:113300200-113301400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr2:113300200-113301400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:113300200-113301600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr2:113300200-113301600	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr2:113300200-113301600	Flanking Active TSS	Fetal Thymus	thymus
29	chr2:113300200-113301800	Flanking Active TSS	Dnd41	blood
30	chr2:113300400-113301400	Flanking Active TSS	HUVEC	blood vessel
31	chr2:113300400-113301400	Flanking Active TSS	Osteobl	bone
32	chr2:113300600-113301400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:113300600-113301400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:113300600-113301400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:113300600-113301400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr2:113300600-113301400	Flanking Active TSS	Liver	Liver
37	chr2:113300600-113301400	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr2:113300600-113301400	Flanking Active TSS	Fetal Brain Female	brain
39	chr2:113300600-113301800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:113300800-113301400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:113300800-113301400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr2:113300800-113301400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr2:113300800-113301400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr2:113300800-113301400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:113300800-113301400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:113300800-113301400	Flanking Active TSS	Fetal Brain Male	brain
47	chr2:113300800-113301400	Flanking Active TSS	Fetal Kidney	kidney
48	chr2:113300800-113301400	Flanking Active TSS	NHDF-Ad	bronchial
49	chr2:113300800-113301600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:113300800-113301600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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