Variant report

Variant	rs4500955
Chromosome Location	chr2:112770798-112770799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10166564	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10171174	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10173553	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10177803	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10180345	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs10186291	0.95[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10187041	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10188642	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10189399	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10199083	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10199616	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10207820	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs10210692	0.95[CEU][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11123073	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1131244	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11676037	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11683409	0.95[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11683421	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11683819	0.95[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11690939	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11887259	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13385764	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13394651	0.95[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13399108	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1516627	0.95[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs1516628	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1554214	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1554215	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1607059	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17042095	0.89[JPT][hapmap]
rs1996322	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1996323	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1996325	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1996326	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1996327	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1996328	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs1996329	0.89[JPT][hapmap]
rs2230515	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2871922	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs35096883	0.82[AMR][1000 genomes]
rs3761700	0.88[JPT][hapmap]
rs3761701	0.95[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes]
rs3811636	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3811637	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3811638	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4303721	0.91[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4305289	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4353657	0.95[CEU][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4374383	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4468823	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs4511729	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4519530	0.91[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4524124	0.95[CEU][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4525705	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4627569	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4643544	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4848256	0.81[EUR][1000 genomes]
rs4848901	0.87[JPT][hapmap]
rs4848908	0.94[JPT][hapmap]
rs4848918	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4848923	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4848933	0.91[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6541971	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs6541998	0.95[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66477683	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66486378	0.81[EUR][1000 genomes]
rs6709662	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6710591	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6711146	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6711987	0.88[JPT][hapmap]
rs6725192	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6726639	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6739294	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs68087924	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7425877	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7564225	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7569614	0.94[JPT][hapmap]
rs7571009	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7571120	0.91[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7579906	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs7588459	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7592909	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7604639	0.95[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7605527	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs869016	0.87[CEU][hapmap]
rs870762	0.91[CEU][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs884448	0.88[JPT][hapmap]
rs908518	0.95[CEU][hapmap];0.88[JPT][hapmap]

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

No data

Chromatin state (count:70 , 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	chr2:112732600-112771200	Strong transcription	Liver	Liver
5	chr2:112733200-112789200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:112741400-112777000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:112741400-112777000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:112742000-112776800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:112744200-112777000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:112744200-112777200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:112744600-112774000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:112753000-112784000	Weak transcription	Fetal Lung	lung
13	chr2:112753600-112771600	Strong transcription	HepG2	liver
14	chr2:112755400-112789200	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:112758200-112789600	Weak transcription	Fetal Kidney	kidney
16	chr2:112759200-112777000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:112761800-112784000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:112762000-112777000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:112762200-112782600	Weak transcription	Esophagus	oesophagus
20	chr2:112765000-112771400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:112765600-112771400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:112765600-112771400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:112765600-112773000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:112765800-112770800	Strong transcription	Aorta	Aorta
25	chr2:112765800-112771400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:112765800-112771400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:112765800-112771400	Strong transcription	Left Ventricle	heart
28	chr2:112765800-112771400	Strong transcription	HUVEC	blood vessel
29	chr2:112765800-112789600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:112766000-112771400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:112766000-112771600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:112766200-112771400	Strong transcription	Brain Anterior Caudate	brain
33	chr2:112766200-112771400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr2:112766800-112777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:112767600-112771200	Strong transcription	Brain Substantia Nigra	brain
36	chr2:112767800-112771400	Strong transcription	Fetal Stomach	stomach
37	chr2:112767800-112771600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:112768000-112789200	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:112768200-112771400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:112768600-112789600	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:112768800-112773600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:112768800-112777000	Weak transcription	Lung	lung
43	chr2:112768800-112778600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:112769000-112770800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:112769000-112776600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:112769000-112776600	Weak transcription	K562	blood
47	chr2:112769000-112779000	Weak transcription	Placenta	Placenta
48	chr2:112769000-112789000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:112769000-112789200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:112769200-112771400	Strong transcription	Duodenum Mucosa	Duodenum

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