Variant report

Variant	rs2306936
Chromosome Location	chr1:113246630-113246631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113246393-113248209	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:113240102-113248907	U87	brain:	n/a	n/a
3	POLR2A	chr1:113246431-113246889	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:113244126-113248331	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:113246557-113246895	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:113246289-113248630	K562	blood:	n/a	n/a
7	POLR2A	chr1:113245402-113248867	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:113240207-113248892	K562	blood:	n/a	n/a
9	POLR2A	chr1:113241110-113248218	K562	blood:	n/a	n/a
10	POLR2A	chr1:113246569-113248289	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:113240680-113249021	K562	blood:	n/a	n/a
12	POLR2A	chr1:113246476-113247104	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:113246263-113248823	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:113242915-113248528	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:113240211-113248533	A549	lung:	n/a	n/a
16	POLR2A	chr1:113246620-113246638	K562	blood:	n/a	n/a
17	POLR2A	chr1:113240649-113246839	K562	blood:	n/a	n/a
18	POLR2A	chr1:113246443-113248182	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:113246315-113246642	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:113240375-113248999	K562	blood:	n/a	n/a
21	POLR2A	chr1:113241165-113248430	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:113246519-113248726	K562	blood:	n/a	n/a
23	POLR2A	chr1:113246180-113250420	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr1:113240783-113246836	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr1:113246409-113248294	K562	blood:	n/a	n/a
26	MTA3	chr1:113246360-113249177	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:113246214-113248908	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr1:113241768-113248472	U87	brain:	n/a	n/a
29	POLR2A	chr1:113240249-113248607	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:113242062-113248544	Hela-S3	cervix:	n/a	n/a
31	ZNF263	chr1:113246407-113250683	HEK293-T-REx	kidney:	n/a	chr1:113247538-113247547 chr1:113247695-113247704 chr1:113247825-113247834 chr1:113247380-113247389
32	POLR2A	chr1:113240102-113248913	U87	brain:	n/a	n/a
33	POLR2A	chr1:113246236-113250578	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:113242838-113248485	MCF-7	breast:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

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	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
6	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
7	chr1:113214590..113222957-chr1:113244863..113253590,39	MCF-7	breast:
8	chr1:113193696..113195497-chr1:113246337..113249077,2	K562	blood:
9	chr1:113246571..113247384-chr14:58710844..58711538,2	Hela-S3	cervix:
10	chr1:113245734..113247821-chr9:139221192..139223376,2	MCF-7	breast:
11	chr1:113167976..113172227-chr1:113246480..113250465,5	K562	blood:
12	chr1:113193696..113198407-chr1:113243250..113250056,8	K562	blood:
13	chr1:113167944..113171007-chr1:113245720..113249508,3	MCF-7	breast:
14	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
15	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

No data

Variant related genes	Relation type
RHOC	TF binding region
ENSG00000235299	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000160360	Chromatin interaction
ENSG00000184599	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11102489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[ASN][1000 genomes]
rs12064734	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12076902	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs17030459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs17030647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3790599	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57646766	0.91[ASN][1000 genomes]
rs74111163	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:121 , 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	chr1:113240400-113247000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:113240400-113247200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:113240600-113246800	Genic enhancers	Colonic Mucosa	Colon
5	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Trunk	muscle
6	chr1:113240600-113247000	Genic enhancers	Fetal Muscle Leg	muscle
7	chr1:113240600-113247200	Genic enhancers	Placenta	Placenta
8	chr1:113240800-113247200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:113241200-113247000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:113241200-113247200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:113241600-113247000	Genic enhancers	Fetal Intestine Small	intestine
12	chr1:113241600-113249200	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:113241800-113247000	Genic enhancers	Colon Smooth Muscle	Colon
14	chr1:113242000-113248000	Enhancers	Primary B cells from cord blood	blood
15	chr1:113242400-113247000	Genic enhancers	Fetal Stomach	stomach
16	chr1:113242400-113247000	Genic enhancers	Spleen	Spleen
17	chr1:113242400-113247000	Genic enhancers	NHLF	lung
18	chr1:113242800-113247000	Enhancers	Brain Substantia Nigra	brain
19	chr1:113242800-113247200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:113242800-113247800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:113243000-113247000	Enhancers	Brain Angular Gyrus	brain
22	chr1:113243200-113246800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr1:113243400-113246800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:113243400-113246800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:113243600-113247000	Genic enhancers	A549	lung
26	chr1:113243800-113247200	Weak transcription	Fetal Brain Female	brain
27	chr1:113244000-113246800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:113244000-113246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:113244000-113246800	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr1:113244000-113246800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:113244000-113247000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
32	chr1:113244000-113247200	Weak transcription	Brain Germinal Matrix	brain
33	chr1:113244200-113246800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:113244200-113246800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:113244200-113246800	Genic enhancers	Stomach Smooth Muscle	stomach
36	chr1:113244200-113247000	Genic enhancers	HSMM	muscle
37	chr1:113244200-113247200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:113244200-113247400	Enhancers	Fetal Heart	heart
39	chr1:113244400-113247000	Weak transcription	Thymus	Thymus
40	chr1:113244400-113247200	Weak transcription	Primary T cells from cord blood	blood
41	chr1:113244400-113247200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:113244600-113246800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:113244600-113246800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:113244600-113247000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:113244600-113247200	Weak transcription	Ovary	ovary
46	chr1:113244800-113246800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:113244800-113247000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:113245000-113246800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:113245000-113247200	Enhancers	Right Atrium	heart
50	chr1:113245200-113247000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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