Variant report

Variant	rs2279499
Chromosome Location	chr1:113247563-113247564
allele	C/T
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	ZBTB7A	chr1:113247330-113248068	K562	blood:	n/a	n/a
2	EP300	chr1:113247503-113248020	SK-N-SH_RA	brain:	n/a	chr1:113247691-113247700 chr1:113247687-113247701
3	RUNX3	chr1:113247291-113248395	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:113247523-113248047	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr1:113247289-113247886	K562	blood:	n/a	n/a
6	MAX	chr1:113247525-113247953	H1-hESC	embryonic stem cell:	n/a	chr1:113247619-113247629
7	ZNF143	chr1:113247528-113248138	K562	blood:	n/a	n/a
8	POLR2A	chr1:113247074-113248127	GM12878	blood:	n/a	n/a
9	IKZF1	chr1:113247412-113248411	GM12878	blood:	n/a	n/a
10	RCOR1	chr1:113247326-113248153	K562	blood:	n/a	n/a
11	TCF12	chr1:113247298-113248582	A549	lung:	n/a	n/a
12	POLR2A	chr1:113246393-113248209	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr1:113247221-113248313	K562	blood:	n/a	n/a
14	STAT5A	chr1:113247495-113247847	GM12878	blood:	n/a	chr1:113247539-113247547
15	POLR2A	chr1:113247419-113248153	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr1:113246913-113248302	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:113240102-113248907	U87	brain:	n/a	n/a
18	RCOR1	chr1:113247440-113248252	GM12878	blood:	n/a	n/a
19	SP1	chr1:113247374-113248322	A549	lung:	n/a	chr1:113247800-113247811 chr1:113247629-113247638 chr1:113247797-113247811 chr1:113247800-113247812 chr1:113247801-113247810 chr1:113247628-113247638 chr1:113247800-113247812 chr1:113247628-113247642
20	IRF1	chr1:113247415-113248398	K562	blood:	n/a	chr1:113247688-113247697
21	ATF2	chr1:113247446-113248342	GM12878	blood:	n/a	n/a
22	TEAD4	chr1:113247132-113249018	K562	blood:	n/a	n/a
23	POLR2A	chr1:113247417-113248218	SK-N-MC	brain:	n/a	n/a
24	MAX	chr1:113247317-113248260	A549	lung:	n/a	chr1:113247387-113247397 chr1:113248122-113248131 chr1:113247619-113247629
25	HDAC2	chr1:113247376-113247885	K562	blood:	n/a	n/a
26	SPI1	chr1:113247471-113247824	K562	blood:	n/a	chr1:113247568-113247581 chr1:113247706-113247719 chr1:113247690-113247703 chr1:113247796-113247809 chr1:113247689-113247702 chr1:113247690-113247703
27	CUX1	chr1:113247529-113248226	GM12878	blood:	n/a	n/a
28	RELA	chr1:113247528-113248136	GM19099	blood:	n/a	n/a
29	MYC	chr1:113247430-113247753	MCF-7	breast:	n/a	chr1:113247619-113247629
30	POLR2A	chr1:113244126-113248331	GM12878	blood:	n/a	n/a
31	ELF1	chr1:113247177-113248108	GM12878	blood:	n/a	chr1:113247691-113247702 chr1:113247689-113247702
32	ELF1	chr1:113247481-113248249	GM12878	blood:	n/a	chr1:113247691-113247702 chr1:113247689-113247702
33	PML	chr1:113247385-113248408	K562	blood:	n/a	n/a
34	POLR2A	chr1:113247250-113248266	GM12878	blood:	n/a	n/a
35	HDAC2	chr1:113247542-113248412	MCF-7	breast:	n/a	n/a
36	HDAC2	chr1:113247436-113248385	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:113247404-113248219	GM12892	blood:	n/a	n/a
38	MYC	chr1:113247489-113247699	HepG2	liver:	n/a	chr1:113247619-113247629
39	TCF7L2	chr1:113247501-113248337	Hela-S3	cervix:	n/a	chr1:113248141-113248155
40	MAZ	chr1:113246923-113250658	IMR90	lung:	n/a	chr1:113247387-113247397 chr1:113248122-113248131
41	POLR2A	chr1:113247468-113248362	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:113247485-113248228	PANC-1	pancreas:	n/a	n/a
43	JUND	chr1:113247392-113248507	K562	blood:	n/a	chr1:113248123-113248131 chr1:113247586-113247594 chr1:113248122-113248133 chr1:113247484-113247494 chr1:113248121-113248132 chr1:113247584-113247595 chr1:113248449-113248456
44	EBF1	chr1:113247281-113248036	GM12878	blood:	n/a	chr1:113247701-113247711 chr1:113247701-113247710 chr1:113247700-113247711 chr1:113247701-113247710
45	GABPA	chr1:113247522-113247873	A549	lung:	n/a	n/a
46	ESR1	chr1:113247168-113247927	ECC-1	luminal epithelium:	n/a	chr1:113247175-113247190 chr1:113247416-113247433
47	MXI1	chr1:113247560-113248313	GM12878	blood:	n/a	n/a
48	GATA3	chr1:113247458-113248490	MCF-7	breast:	n/a	chr1:113247689-113247699 chr1:113247602-113247609
49	STAT3	chr1:113247454-113248259	MCF10A-Er-Src	breast:	n/a	chr1:113247539-113247547
50	TBL1XR1	chr1:113247463-113248210	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113160723..113165170-chr1:113245654..113250392,12	K562	blood:
3	chr1:113246571..113250786-chr1:113261233..113263716,3	K562	blood:
4	chr1:113244850..113247809-chr17:57917279..57920025,2	MCF-7	breast:
5	chr1:113247359..113247865-chr20:47894503..47895440,2	Hela-S3	cervix:
6	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
7	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
8	chr1:113214590..113222957-chr1:113244863..113253590,39	MCF-7	breast:
9	chr1:113247278..113248218-chr16:28834319..28834859,2	Hela-S3	cervix:
10	chr1:113193696..113195497-chr1:113246337..113249077,2	K562	blood:
11	chr1:113245734..113247821-chr9:139221192..139223376,2	MCF-7	breast:
12	chr1:113167976..113172227-chr1:113246480..113250465,5	K562	blood:
13	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
14	chr1:113008643..113012570-chr1:113247176..113250622,4	MCF-7	breast:
15	chr1:113193696..113198407-chr1:113243250..113250056,8	K562	blood:
16	chr1:113167944..113171007-chr1:113245720..113249508,3	MCF-7	breast:
17	chr1:113247318..113247865-chr2:38303280..38304066,2	Hela-S3	cervix:
18	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
19	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:
20	chr1:113247324..113248167-chr2:96873509..96874450,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST7L-6	chr1:113247262-113247790	NONHSAT005278

Variant related genes	Relation type
RHOC	TF binding region
ENSG00000238975	Chromatin interaction
ENSG00000168488	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000124201	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000177410	Chromatin interaction
ENSG00000232973	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000184599	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000160360	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000138061	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1106287	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1110042	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11102513	0.83[ASN][1000 genomes]
rs11102514	0.83[ASN][1000 genomes]
rs11102520	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11102522	0.90[ASN][1000 genomes]
rs12030612	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12030641	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12040988	0.83[ASN][1000 genomes]
rs12120956	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12122980	0.83[ASN][1000 genomes]
rs12126684	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12126971	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130243	0.83[ASN][1000 genomes]
rs12133583	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12406282	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12728311	0.80[ASN][1000 genomes]
rs12756815	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17030613	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17030651	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2009056	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306937	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306940	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2887882	0.83[ASN][1000 genomes]
rs34848593	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3748656	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3795819	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61818802	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61818805	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6679	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs883593	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9308256	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active 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 miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv872157	chr1:113247467-113265819	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279499	ST7L	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:113241600-113249200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:113242000-113248000	Enhancers	Primary B cells from cord blood	blood
4	chr1:113242800-113247800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:113245400-113247800	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:113246400-113249000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:113246600-113247600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:113246600-113247600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:113246600-113247600	Enhancers	Small Intestine	intestine
10	chr1:113246600-113249000	Flanking Active TSS	Hela-S3	cervix
11	chr1:113246800-113247600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
12	chr1:113246800-113247600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:113246800-113247600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr1:113246800-113247600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:113246800-113247600	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:113246800-113247800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr1:113246800-113248000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr1:113246800-113248600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:113246800-113248600	Flanking Active TSS	HMEC	breast
20	chr1:113246800-113248800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:113246800-113248800	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr1:113246800-113249000	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr1:113246800-113249000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr1:113246800-113249000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr1:113246800-113249600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr1:113246800-113249600	Flanking Active TSS	Dnd41	blood
27	chr1:113247000-113247600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
28	chr1:113247000-113247600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr1:113247000-113247600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
30	chr1:113247000-113247600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:113247000-113247600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:113247000-113247600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:113247000-113247600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:113247000-113247600	Flanking Active TSS	Colonic Mucosa	Colon
35	chr1:113247000-113247600	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr1:113247000-113247600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
37	chr1:113247000-113247800	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:113247000-113248000	Flanking Active TSS	Stomach Mucosa	stomach
39	chr1:113247000-113248000	Flanking Active TSS	HSMM	muscle
40	chr1:113247000-113248600	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr1:113247000-113248600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr1:113247000-113248800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:113247000-113248800	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr1:113247000-113248800	Flanking Active TSS	Left Ventricle	heart
45	chr1:113247000-113248800	Flanking Active TSS	Right Ventricle	heart
46	chr1:113247000-113248800	Flanking Active TSS	HUVEC	blood vessel
47	chr1:113247000-113248800	Flanking Active TSS	NH-A	brain
48	chr1:113247000-113249000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:113247000-113249000	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr1:113247000-113249000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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