Variant report

Variant	rs1052117
Chromosome Location	chr2:101186088-101186089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:101177817..101179680-chr2:101183661..101186374,4	K562	blood:
2	chr2:101178645..101181337-chr2:101184679..101187696,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115539	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10178491	1.00[ASN][1000 genomes]
rs10190324	1.00[ASN][1000 genomes]
rs10200086	0.82[ASN][1000 genomes]
rs1114285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11681805	0.92[ASN][1000 genomes]
rs11691661	1.00[ASN][1000 genomes]
rs12469332	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12616005	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12618862	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12622226	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13393125	0.82[ASN][1000 genomes]
rs13418741	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1401753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1533655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1589246	1.00[JPT][hapmap]
rs17024338	1.00[JPT][hapmap]
rs2139402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309846	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309848	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28560372	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28673254	0.85[AMR][1000 genomes]
rs28694778	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2970997	1.00[JPT][hapmap]
rs2971007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4850940	1.00[ASN][1000 genomes]
rs4851332	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4851333	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4851334	1.00[ASN][1000 genomes]
rs4851335	1.00[ASN][1000 genomes]
rs4851337	1.00[ASN][1000 genomes]
rs4851338	1.00[ASN][1000 genomes]
rs58420974	1.00[ASN][1000 genomes]
rs61370232	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62155213	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542968	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542969	1.00[JPT][hapmap]
rs66689046	0.82[ASN][1000 genomes]
rs67061569	1.00[ASN][1000 genomes]
rs6739992	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746622	0.92[AMR][1000 genomes]
rs6747613	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748900	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557603	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560366	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7578708	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7594904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7596475	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv834312	chr2:101044438-101238166	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv961462	chr2:101183451-101186190	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101180200-101194400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:101180400-101186200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:101180400-101187200	Weak transcription	Fetal Kidney	kidney
4	chr2:101180400-101188400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:101180600-101187800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:101180600-101192600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:101180600-101192800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:101180600-101193400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:101180600-101194400	Weak transcription	NHDF-Ad	bronchial
10	chr2:101180600-101197800	Weak transcription	Stomach Mucosa	stomach
11	chr2:101180800-101187200	Weak transcription	K562	blood
12	chr2:101180800-101195600	Weak transcription	Fetal Heart	heart
13	chr2:101180800-101195800	Strong transcription	Fetal Stomach	stomach
14	chr2:101180800-101196800	Weak transcription	NHLF	lung
15	chr2:101180800-101197000	Weak transcription	Colonic Mucosa	Colon
16	chr2:101180800-101197200	Weak transcription	Small Intestine	intestine
17	chr2:101181000-101195800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr2:101181200-101191200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:101181400-101187400	Weak transcription	Pancreas	Pancrea
20	chr2:101181400-101187800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:101181400-101188200	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:101181400-101195800	Strong transcription	Fetal Muscle Leg	muscle
23	chr2:101181400-101196200	Weak transcription	Gastric	stomach
24	chr2:101181400-101196800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:101181600-101188200	Weak transcription	Esophagus	oesophagus
26	chr2:101181600-101196600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:101181600-101197200	Weak transcription	Brain Angular Gyrus	brain
28	chr2:101182000-101194600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:101182600-101186200	Strong transcription	Brain Hippocampus Middle	brain
30	chr2:101182600-101187000	Strong transcription	Primary B cells from cord blood	blood
31	chr2:101182600-101187800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:101182600-101189200	Strong transcription	Brain Germinal Matrix	brain
33	chr2:101182600-101191600	Strong transcription	Dnd41	blood
34	chr2:101182600-101192800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:101182600-101193600	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:101182600-101194200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:101182600-101195800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:101182600-101195800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:101182800-101186400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:101182800-101186400	Strong transcription	Brain Anterior Caudate	brain
41	chr2:101182800-101186400	Strong transcription	Fetal Brain Female	brain
42	chr2:101182800-101187200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:101182800-101188400	Strong transcription	Left Ventricle	heart
44	chr2:101182800-101188600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr2:101182800-101189800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:101182800-101192200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:101182800-101192400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:101182800-101192800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:101182800-101193400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:101182800-101194600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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