Variant report

Variant	rs12144044
Chromosome Location	chr1:113248791-113248792
allele	A/C
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	chr1:113240102-113248907	U87	brain:	n/a	n/a
2	TEAD4	chr1:113247132-113249018	K562	blood:	n/a	n/a
3	POLR2A	chr1:113248771-113248829	ProgFib	skin:	n/a	n/a
4	MAZ	chr1:113246923-113250658	IMR90	lung:	n/a	chr1:113247387-113247397 chr1:113248122-113248131
5	POLR2A	chr1:113247193-113249029	K562	blood:	n/a	n/a
6	POLR2A	chr1:113247355-113248949	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr1:113247261-113250309	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:113245402-113248867	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:113240207-113248892	K562	blood:	n/a	n/a
10	POLR2A	chr1:113240680-113249021	K562	blood:	n/a	n/a
11	POLR2A	chr1:113246263-113248823	Hela-S3	cervix:	n/a	n/a
12	JUN	chr1:113247085-113251456	K562	blood:	n/a	chr1:113248123-113248131 chr1:113247586-113247594 chr1:113248122-113248133 chr1:113247484-113247494 chr1:113247584-113247595 chr1:113248449-113248456
13	POLR2A	chr1:113247167-113250323	K562	blood:	n/a	n/a
14	STAT5A	chr1:113247115-113249012	GM12878	blood:	n/a	chr1:113247539-113247547
15	UBTF	chr1:113247221-113250349	K562	blood:	n/a	n/a
16	SMARCB1	chr1:113247096-113250480	Hela-S3	cervix:	n/a	chr1:113247585-113247594
17	NR2F2	chr1:113247087-113250506	K562	blood:	n/a	n/a
18	POLR2A	chr1:113240375-113248999	K562	blood:	n/a	n/a
19	SMARCC1	chr1:113247047-113250566	Hela-S3	cervix:	n/a	chr1:113247585-113247594
20	POLR2A	chr1:113246180-113250420	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:113247015-113250256	IMR90	lung:	n/a	n/a
22	TAF1	chr1:113248632-113249017	K562	blood:	n/a	n/a
23	POLR2A	chr1:113247039-113249062	K562	blood:	n/a	n/a
24	MTA3	chr1:113246360-113249177	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:113246963-113250480	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr1:113246214-113248908	HUVEC	blood vessel:	n/a	n/a
27	ZNF263	chr1:113246407-113250683	HEK293-T-REx	kidney:	n/a	chr1:113247538-113247547 chr1:113247695-113247704 chr1:113247825-113247834 chr1:113247380-113247389
28	POLR2A	chr1:113240102-113248913	U87	brain:	n/a	n/a
29	POLR2A	chr1:113246661-113248828	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:113246236-113250578	Hela-S3	cervix:	n/a	n/a
31	HEY1	chr1:113246845-113248878	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113248698..113251078-chr1:113932422..113935147,2	MCF-7	breast:
3	chr1:113160723..113165170-chr1:113245654..113250392,12	K562	blood:
4	chr1:113246571..113250786-chr1:113261233..113263716,3	K562	blood:
5	chr1:112938761..112941761-chr1:113247568..113249753,3	MCF-7	breast:
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	chr1:113193696..113195497-chr1:113246337..113249077,2	K562	blood:
10	chr1:113167976..113172227-chr1:113246480..113250465,5	K562	blood:
11	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
12	chr1:113008643..113012570-chr1:113247176..113250622,4	MCF-7	breast:
13	chr1:113193696..113198407-chr1:113243250..113250056,8	K562	blood:
14	chr1:113167944..113171007-chr1:113245720..113249508,3	MCF-7	breast:
15	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
16	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

Variant related genes	Relation type
RHOC	TF binding region
ENSG00000155363	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000081026	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000184599	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12138335	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12401734	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12402929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12739994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12750621	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932529	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932537	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36022459	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3795820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3806441	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806442	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806443	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537740	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6537741	1.00[JPT][hapmap]
rs6537742	0.82[JPT][hapmap]
rs6658555	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6668533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6681371	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7415988	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	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
11	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	esv3358595	chr1:113248454-113251002	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12144044	DRAM2	cis	cerebellum	SCAN
rs12144044	BCL2L15	cis	parietal	SCAN
rs12144044	RHOC	cis	parietal	SCAN
rs12144044	DENND2C	cis	parietal	SCAN
rs12144044	ST7L	cis	multi-tissue	Pritchard
rs12144044	MOV10	cis	parietal	SCAN
rs12144044	HBXIP	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113241600-113249200	Enhancers	Primary B cells from peripheral blood	blood
2	chr1:113246400-113249000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:113246600-113249000	Flanking Active TSS	Hela-S3	cervix
4	chr1:113246800-113248800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:113246800-113248800	Flanking Active TSS	Rectal Smooth Muscle	rectum
6	chr1:113246800-113249000	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr1:113246800-113249000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:113246800-113249000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr1:113246800-113249600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr1:113246800-113249600	Flanking Active TSS	Dnd41	blood
11	chr1:113247000-113248800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:113247000-113248800	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr1:113247000-113248800	Flanking Active TSS	Left Ventricle	heart
14	chr1:113247000-113248800	Flanking Active TSS	Right Ventricle	heart
15	chr1:113247000-113248800	Flanking Active TSS	HUVEC	blood vessel
16	chr1:113247000-113248800	Flanking Active TSS	NH-A	brain
17	chr1:113247000-113249000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:113247000-113249000	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr1:113247000-113249000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr1:113247000-113249000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr1:113247000-113249000	Flanking Active TSS	Fetal Lung	lung
22	chr1:113247000-113249000	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr1:113247000-113249000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr1:113247000-113249000	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr1:113247000-113249600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:113247200-113248800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:113247200-113248800	Flanking Active TSS	Osteobl	bone
28	chr1:113247200-113249000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:113247200-113249000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr1:113247200-113249000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:113247200-113249000	Flanking Active TSS	K562	blood
32	chr1:113247200-113249400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:113247200-113249400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:113247200-113250400	Active TSS	Aorta	Aorta
35	chr1:113247400-113248800	Flanking Active TSS	Fetal Stomach	stomach
36	chr1:113247400-113248800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr1:113247400-113249000	Flanking Active TSS	Liver	Liver
38	chr1:113247400-113249000	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr1:113247400-113249000	Flanking Active TSS	Placenta	Placenta
40	chr1:113247400-113249000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr1:113247400-113249600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:113247400-113250200	Active TSS	Psoas Muscle	Psoas
43	chr1:113247400-113250400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:113247400-113250400	Active TSS	Ovary	ovary
45	chr1:113247400-113250400	Active TSS	Right Atrium	heart
46	chr1:113247400-113250400	Active TSS	A549	lung
47	chr1:113247600-113248800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr1:113247600-113248800	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr1:113247600-113249600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
50	chr1:113247600-113250200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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