Variant report

Variant	rs13387346
Chromosome Location	chr2:112773057-112773058
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	MAX	chr2:112772785-112773237	MCF-7	breast:	n/a	n/a
2	TCF7L2	chr2:112772827-112773218	MCF-7	breast:	n/a	chr2:112773051-112773065
3	GATA2	chr2:112772841-112773302	HUVEC	blood vessel:	n/a	n/a
4	FOS	chr2:112772834-112773193	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr2:112772813-112773535	HUVEC	blood vessel:	n/a	chr2:112773278-112773289
6	HDAC2	chr2:112772743-112773255	MCF-7	breast:	n/a	n/a
7	FOS	chr2:112772889-112773143	MCF10A-Er-Src	breast:	n/a	n/a
8	GATA3	chr2:112772741-112773328	MCF-7	breast:	n/a	n/a
9	GATA3	chr2:112772597-112773398	MCF-7	breast:	n/a	n/a
10	FOSL2	chr2:112772744-112773249	MCF-7	breast:	n/a	n/a
11	NR2F2	chr2:112772786-112773229	MCF-7	breast:	n/a	n/a
12	MYC	chr2:112772888-112773186	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112728932..112731897-chr2:112771054..112773671,2	MCF-7	breast:

Variant related genes	Relation type
MERTK	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10084408	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs10165614	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap]
rs10165940	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10168067	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10174680	1.00[GIH][hapmap]
rs10175344	0.80[EUR][1000 genomes]
rs10179948	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10180086	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10181117	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10182764	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10182931	0.80[EUR][1000 genomes]
rs10185394	0.82[EUR][1000 genomes]
rs10185747	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs10190471	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10198007	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205067	1.00[CHD][hapmap]
rs10205793	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10206255	1.00[GIH][hapmap]
rs10207237	0.82[EUR][1000 genomes]
rs10209260	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap]
rs10211152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13313775	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13383743	0.80[EUR][1000 genomes]
rs13394094	0.80[EUR][1000 genomes]
rs13396030	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13397194	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401834	0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13402707	1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13404771	1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13406390	1.00[CHD][hapmap]
rs13411851	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13413103	0.82[EUR][1000 genomes]
rs13414207	0.82[EUR][1000 genomes]
rs13416895	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13418394	1.00[GIH][hapmap]
rs13419523	1.00[CHD][hapmap]
rs13421261	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13430221	0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13432863	1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2230517	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28529268	1.00[AMR][1000 genomes]
rs56264210	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6723289	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6723394	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6735717	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72823495	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72825621	0.82[EUR][1000 genomes]
rs72825696	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72829620	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9631022	0.80[EUR][1000 genomes]
rs9631023	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv999746	chr2:112691270-112796083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv2760607	chr2:112691282-112803423	Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv431491	chr2:112699350-112793981	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv515698	chr2:112699350-112795908	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv933392	chr2:112747230-112792349	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13387346	CXorf61	trans	lymphoblastoid	seeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112713200-112790600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:112718400-112776400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:112723400-112789200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:112733200-112789200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:112741400-112777000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:112741400-112777000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:112742000-112776800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:112744200-112777000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:112744200-112777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:112744600-112774000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:112753000-112784000	Weak transcription	Fetal Lung	lung
12	chr2:112755400-112789200	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:112758200-112789600	Weak transcription	Fetal Kidney	kidney
14	chr2:112759200-112777000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:112761800-112784000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:112762000-112777000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:112762200-112782600	Weak transcription	Esophagus	oesophagus
18	chr2:112765800-112789600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:112766800-112777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:112768000-112789200	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:112768600-112789600	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:112768800-112773600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:112768800-112777000	Weak transcription	Lung	lung
24	chr2:112768800-112778600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:112769000-112776600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:112769000-112776600	Weak transcription	K562	blood
27	chr2:112769000-112779000	Weak transcription	Placenta	Placenta
28	chr2:112769000-112789000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:112769000-112789200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:112769200-112780000	Weak transcription	Right Ventricle	heart
31	chr2:112769200-112781200	Weak transcription	Pancreas	Pancrea
32	chr2:112769200-112788400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:112769200-112789200	Weak transcription	Adipose Nuclei	Adipose
34	chr2:112769600-112777000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:112769600-112778400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:112769600-112791200	Weak transcription	Colonic Mucosa	Colon
37	chr2:112769800-112779600	Weak transcription	Spleen	Spleen
38	chr2:112770000-112782400	Weak transcription	Ovary	ovary
39	chr2:112770200-112781400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:112770200-112789400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:112770400-112781800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:112770600-112787600	Weak transcription	Brain Angular Gyrus	brain
43	chr2:112770800-112776600	Weak transcription	Aorta	Aorta
44	chr2:112771200-112777000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:112771200-112778800	Weak transcription	Brain Substantia Nigra	brain
46	chr2:112771400-112773800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:112771400-112774000	Weak transcription	Brain Anterior Caudate	brain
48	chr2:112771400-112775200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:112771400-112776000	Weak transcription	Fetal Intestine Large	intestine
50	chr2:112771400-112776000	Weak transcription	Stomach Smooth Muscle	stomach

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