Variant report

Variant	rs849749
Chromosome Location	chr1:228296745-228296746
allele	A/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	POLR2A	chr1:228296659-228297799	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:228296622-228298090	GM12878	blood:	n/a	n/a
3	SP1	chr1:228296744-228297430	GM12878	blood:	n/a	chr1:228297140-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297120-228297129 chr1:228297119-228297131 chr1:228297087-228297097 chr1:228297140-228297149 chr1:228297141-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297088-228297097 chr1:228297119-228297131 chr1:228297140-228297150 chr1:228297121-228297130
4	TCF12	chr1:228296692-228297526	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:228296723-228297445	GM18526	blood:	n/a	n/a
6	TAF1	chr1:228296725-228297393	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr1:228296645-228297332	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:228296726-228297338	A549	lung:	n/a	n/a
9	SRF	chr1:228296642-228297331	ECC-1	luminal epithelium:	n/a	chr1:228297184-228297194 chr1:228297091-228297101 chr1:228297140-228297150
10	CTCF	chr1:228296680-228296830	HAc	cerebellar:	n/a	n/a
11	POLR2A	chr1:228296432-228297439	K562	blood:	n/a	n/a
12	POLR2A	chr1:228296741-228297434	K562	blood:	n/a	n/a
13	POLR2A	chr1:228296531-228297510	ECC-1	luminal epithelium:	n/a	n/a
14	JUND	chr1:228296728-228297347	A549	lung:	n/a	n/a
15	POLR2A	chr1:228296631-228297505	MCF-7	breast:	n/a	n/a
16	SP1	chr1:228296387-228297568	HCT-116	colon:	n/a	chr1:228297140-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297120-228297129 chr1:228297119-228297131 chr1:228297087-228297097 chr1:228297140-228297149 chr1:228297141-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297088-228297097 chr1:228297119-228297131 chr1:228297140-228297150 chr1:228297121-228297130
17	POLR2A	chr1:228296611-228297758	GM19193	blood:	n/a	n/a
18	E2F4	chr1:228296586-228297268	K562	blood:	n/a	chr1:228297144-228297154 chr1:228297184-228297194 chr1:228297096-228297105 chr1:228297120-228297132 chr1:228297091-228297101
19	MTA3	chr1:228296665-228297065	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:228296721-228297595	GM15510	blood:	n/a	n/a
21	TAF1	chr1:228296703-228297487	H1-neurons	neurons:	n/a	n/a
22	ETS1	chr1:228296744-228297439	K562	blood:	n/a	n/a
23	CEBPD	chr1:228296723-228297449	HepG2	liver:	n/a	n/a
24	EBF1	chr1:228295768-228297810	GM12878	blood:	n/a	chr1:228296439-228296450
25	POLR2A	chr1:228296738-228298047	GM12878	blood:	n/a	n/a
26	HCFC1	chr1:228296254-228297617	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:228296726-228297397	A549	lung:	n/a	n/a
28	ATF3	chr1:228296602-228297203	K562	blood:	n/a	chr1:228297098-228297107
29	POLR2A	chr1:228296507-228297420	HL-60	blood:	n/a	n/a
30	POLR2A	chr1:228296604-228297617	MCF-7	breast:	n/a	n/a
31	POLR2A	chr1:228296742-228297116	GM12891	blood:	n/a	n/a
32	SIN3A	chr1:228296472-228297371	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:228296631-228297421	Hela-S3	cervix:	n/a	n/a
34	SRF	chr1:228296646-228297444	MCF-7	breast:	n/a	chr1:228297184-228297194 chr1:228297091-228297101 chr1:228297140-228297150
35	POLR2A	chr1:228296624-228297485	MCF-7	breast:	n/a	n/a
36	POLR2A	chr1:228296684-228297371	H1-hESC	embryonic stem cell:	n/a	n/a
37	CUX1	chr1:228296598-228297072	K562	blood:	n/a	n/a
38	POLR2A	chr1:228296584-228297766	PBDE	blood:	n/a	n/a
39	HNF4A	chr1:228296741-228297523	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:228296541-228297489	GM12878	blood:	n/a	n/a
41	ATF2	chr1:228296734-228297356	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:228296636-228297400	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr1:228296595-228297531	HUVEC	blood vessel:	n/a	n/a
44	TRIM28	chr1:228296702-228297278	K562	blood:	n/a	n/a
45	FOSL2	chr1:228296583-228297208	A549	lung:	n/a	n/a
46	TBP	chr1:228296740-228297365	HepG2	liver:	n/a	n/a
47	EGR1	chr1:228296745-228297434	ECC-1	luminal epithelium:	n/a	chr1:228297139-228297149 chr1:228297055-228297062 chr1:228297150-228297163 chr1:228297140-228297150 chr1:228297049-228297062
48	SIX5	chr1:228296530-228297223	A549	lung:	n/a	n/a
49	HDAC2	chr1:228296714-228297143	K562	blood:	n/a	n/a
50	POLR2A	chr1:228296616-228297371	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228295623..228298108-chr1:228335544..228338438,2	MCF-7	breast:
2	chr1:228294222..228297212-chr1:228327852..228330069,2	MCF-7	breast:
3	chr1:228295318..228298683-chr1:228360322..228363984,4	K562	blood:
4	chr1:228295479..228298124-chr1:228352385..228354527,2	MCF-7	breast:
5	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
6	chr1:228296521..228297220-chr3:150321016..150321544,2	NB4	blood:
7	chr1:228292983..228294840-chr1:228295520..228297774,2	MCF-7	breast:
8	chr1:228274118..228278669-chr1:228294195..228297645,6	MCF-7	breast:
9	chr1:228296521..228297564-chr1:228327615..228328500,3	Hela-S3	cervix:
10	chr1:228293945..228298846-chr1:228325398..228330582,13	K562	blood:
11	chr1:228294705..228298588-chr1:228325821..228329680,6	MCF-7	breast:
12	chr1:228295591..228297111-chr1:228358549..228360057,2	K562	blood:
13	chr1:228296537..228297467-chr15:75493986..75494523,2	Hela-S3	cervix:
14	chr1:228296738..228297414-chr7:44836178..44836722,2	NB4	blood:
15	chr1:228295286..228298610-chr1:228351640..228355026,4	K562	blood:
16	chr1:228294689..228298417-chr1:228352364..228354856,6	MCF-7	breast:
17	chr1:228295402..228297803-chr1:228330568..228332279,2	MCF-7	breast:
18	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:
19	chr1:228295585..228298584-chr1:228645620..228647778,2	K562	blood:
20	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:
21	chr1:228270227..228270808-chr1:228296563..228297459,2	NB4	blood:
22	chr1:228295585..228298429-chr1:228645232..228648455,3	K562	blood:
23	chr1:228295500..228297827-chr1:228593936..228595478,2	K562	blood:

Variant related genes	Relation type
C1orf35	TF binding region
MRPL55	TF binding region
ENSG00000143793	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000196262	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000231563	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1059778	0.83[TSI][hapmap]
rs10753445	0.83[TSI][hapmap]
rs10916268	0.85[TSI][hapmap]
rs12084338	0.87[TSI][hapmap]
rs12130630	0.81[EUR][1000 genomes]
rs12134624	0.83[GIH][hapmap];0.82[LWK][hapmap];0.87[TSI][hapmap]
rs12564763	0.85[TSI][hapmap]
rs1620111	0.81[TSI][hapmap]
rs17640616	0.83[TSI][hapmap]
rs1771487	0.81[TSI][hapmap]
rs2066237	0.82[TSI][hapmap]
rs2313601	0.81[TSI][hapmap]
rs2313602	0.85[TSI][hapmap]
rs28634124	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3121310	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs4653907	0.84[ASN][1000 genomes]
rs4653917	0.83[GIH][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap]
rs6426492	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[ASN][1000 genomes]
rs6682260	0.83[GIH][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs708123	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs72757811	0.81[EUR][1000 genomes]
rs7512209	0.85[TSI][hapmap]
rs752107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7523917	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7537636	0.85[TSI][hapmap]
rs7539762	0.83[GIH][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap]
rs766972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs822725	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs822739	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs822740	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
12	nsv482143	chr1:228294380-228297013	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs849749	IBA57	cis	Whole Blood	GTEx
rs849749	GUK1	cis	parietal	SCAN
rs849749	TMEM63A	cis	cerebellum	SCAN
rs849749	OBSCN	cis	Esophagus Mucosa	GTEx
rs849749	OBSCN	cis	Skin Sun Exposed Lower leg	GTEx
rs849749	ACBD3	cis	cerebellum	SCAN
rs849749	WDR26	cis	cerebellum	SCAN
rs849749	ITPKB	cis	cerebellum	SCAN
rs849749	MRPL55	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228295800-228296800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:228295800-228296800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:228295800-228296800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:228295800-228296800	Flanking Active TSS	Liver	Liver
5	chr1:228295800-228296800	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr1:228295800-228296800	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr1:228295800-228296800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:228295800-228297000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:228295800-228297000	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr1:228295800-228297400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:228295800-228297800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:228296000-228296800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:228296000-228296800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr1:228296000-228296800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:228296000-228296800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:228296000-228296800	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr1:228296000-228296800	Flanking Active TSS	Fetal Brain Female	brain
18	chr1:228296000-228296800	Flanking Active TSS	Fetal Thymus	thymus
19	chr1:228296000-228296800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr1:228296000-228296800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr1:228296000-228296800	Flanking Active TSS	Osteobl	bone
22	chr1:228296000-228297400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr1:228296000-228297600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:228296000-228297600	Active TSS	A549	lung
25	chr1:228296000-228298000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:228296000-228298000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr1:228296000-228298200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr1:228296200-228296800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:228296200-228296800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:228296200-228296800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr1:228296200-228296800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr1:228296200-228296800	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr1:228296200-228296800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr1:228296200-228296800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr1:228296200-228296800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:228296200-228296800	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr1:228296200-228296800	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr1:228296200-228296800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr1:228296200-228296800	Flanking Active TSS	Fetal Brain Male	brain
40	chr1:228296200-228296800	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr1:228296200-228296800	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr1:228296200-228296800	Flanking Active TSS	Placenta	Placenta
43	chr1:228296200-228296800	Flanking Active TSS	Fetal Stomach	stomach
44	chr1:228296200-228296800	Flanking Active TSS	Thymus	Thymus
45	chr1:228296200-228297000	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr1:228296200-228297000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:228296200-228297000	Flanking Active TSS	Colonic Mucosa	Colon
48	chr1:228296200-228297000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr1:228296200-228297400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:228296200-228297600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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