Variant report

Variant	rs17724559
Chromosome Location	chr12:83178421-83178422
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	chr12:83168957..83170901-chr12:83176146..83179018,2	K562	blood:
2	chr12:83080290..83082934-chr12:83176093..83178642,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179104	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10746257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10746258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10862508	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10862510	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11115425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11115429	0.94[ASN][1000 genomes]
rs11115432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12298979	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12367228	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12368738	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427130	0.95[ASN][1000 genomes]
rs17009991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17009995	0.83[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs17724637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136137	0.99[ASN][1000 genomes]
rs4491313	0.99[ASN][1000 genomes]
rs4565970	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6539691	0.98[ASN][1000 genomes]
rs6539692	0.99[ASN][1000 genomes]
rs7133807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7307968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7309393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs73358224	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953496	1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs7955825	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:61 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv2755991	chr12:83105631-83248605	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv469491	chr12:83108395-83203742	Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv559543	chr12:83108395-83203742	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv2754173	chr12:83125000-83245838	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv2754509	chr12:83133090-83203742	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv999149	chr12:83137872-83206342	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	nsv1041674	chr12:83162082-83207782	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	esv2754376	chr12:83166800-83203742	Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	nsv1037678	chr12:83166800-83207782	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	esv2760932	chr12:83166800-83208125	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv1046528	chr12:83166800-83215381	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	esv1003105	chr12:83166821-83213521	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	esv2754616	chr12:83166956-83203742	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	nsv899350	chr12:83166956-83203742	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
23	nsv559544	chr12:83166956-83206342	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
24	nsv1040659	chr12:83166956-83207782	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
25	nsv899351	chr12:83166956-83220039	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
26	esv2756046	chr12:83166956-83245838	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
27	esv2755875	chr12:83166956-83248605	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
28	nsv430520	chr12:83166956-83271602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
29	esv1008090	chr12:83167353-83212805	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
30	nsv1051173	chr12:83168049-83203602	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
31	nsv1038818	chr12:83168049-83203742	ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
32	nsv1036837	chr12:83168049-83206208	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
33	nsv1041180	chr12:83168049-83207782	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
34	esv992885	chr12:83168049-83207794	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
35	nsv1044111	chr12:83168049-83215381	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
36	esv2757513	chr12:83168113-83201615	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
37	esv2752585	chr12:83168113-83203742	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
38	esv2755644	chr12:83168113-83203742	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
39	nsv1035729	chr12:83168113-83207782	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
40	esv30004	chr12:83168113-83208383	Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
41	esv2752707	chr12:83168113-83245838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
42	esv2753376	chr12:83168113-83245838	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
43	esv2754178	chr12:83168113-83245838	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
44	nsv559545	chr12:83168616-83191478	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
45	nsv559546	chr12:83168616-83192895	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
46	nsv559547	chr12:83168616-83197515	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
47	nsv559548	chr12:83168616-83205152	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
48	nsv516625	chr12:83168616-83206342	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
49	nsv469492	chr12:83168616-83206342	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
50	nsv559549	chr12:83168616-83206342	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83153200-83198600	Weak transcription	Fetal Intestine Small	intestine
2	chr12:83157200-83196000	Weak transcription	Fetal Muscle Leg	muscle
3	chr12:83169200-83182600	Weak transcription	Fetal Stomach	stomach
4	chr12:83169400-83189400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:83172800-83181200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:83174200-83179600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr12:83174400-83181000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:83175000-83178800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:83175000-83180400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:83175600-83178600	Enhancers	Brain Angular Gyrus	brain
11	chr12:83175600-83181000	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr12:83175800-83180200	Enhancers	Brain Anterior Caudate	brain
13	chr12:83175800-83180800	Enhancers	Brain Substantia Nigra	brain
14	chr12:83175800-83181000	Enhancers	Brain Hippocampus Middle	brain
15	chr12:83175800-83181600	Enhancers	Brain Cingulate Gyrus	brain
16	chr12:83176000-83181400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr12:83176600-83179400	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:83176600-83179800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:83177200-83179400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:83177200-83182200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:83177400-83179400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:83177600-83179800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:83177800-83183800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:83178000-83179200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr12:83178000-83179800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr12:83178000-83180000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr12:83178200-83178600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:83178200-83178800	Enhancers	Adipose Nuclei	Adipose
29	chr12:83178200-83182200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:83178200-83185400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:83178400-83178600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:83178400-83178600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:83178400-83179400	Weak transcription	Fetal Lung	lung

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