Variant report

Variant	rs1548877
Chromosome Location	chr2:39999157-39999158
allele	A/G
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	STAT3	chr2:39998999-39999406	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:39999156-39999497	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39997806..40003955-chr2:40003961..40007756,6	MCF-7	breast:
2	chr2:39981401..39983374-chr2:39998682..40001306,2	K562	blood:
3	chr2:39541547..39543631-chr2:39997665..39999926,2	K562	blood:

Variant related genes	Relation type
THUMPD2	TF binding region
ENSG00000138050	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10164984	0.86[EUR][1000 genomes]
rs10169390	0.84[EUR][1000 genomes]
rs10174709	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10206408	0.84[ASN][1000 genomes]
rs10207589	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10211306	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1035138	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1035139	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11124691	0.85[ASN][1000 genomes]
rs11124692	0.83[EUR][1000 genomes]
rs11124693	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11684302	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12470473	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12617624	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12620957	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623462	0.88[ASN][1000 genomes]
rs12623545	0.88[ASN][1000 genomes]
rs12624217	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712653	0.88[ASN][1000 genomes]
rs12712656	0.86[EUR][1000 genomes]
rs13026313	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13400213	0.81[EUR][1000 genomes]
rs13425906	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13428837	0.86[EUR][1000 genomes]
rs17478972	0.86[EUR][1000 genomes]
rs1861243	0.87[EUR][1000 genomes]
rs1861258	0.89[EUR][1000 genomes]
rs1986876	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2041735	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2058620	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2110656	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2192685	0.82[EUR][1000 genomes]
rs2373689	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2540226	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2540227	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2540228	0.89[EUR][1000 genomes]
rs2716727	0.80[ASN][1000 genomes]
rs2716729	0.89[EUR][1000 genomes]
rs2716730	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35761077	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732121	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732122	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4670955	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4670956	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670957	0.84[ASN][1000 genomes]
rs4670958	0.83[ASN][1000 genomes]
rs4670959	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59756273	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6544242	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6719179	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6722610	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6731026	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731450	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6747842	0.90[ASN][1000 genomes]
rs6750252	0.89[ASN][1000 genomes]
rs6758453	0.89[ASN][1000 genomes]
rs727376	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560642	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7581406	0.86[ASN][1000 genomes]
rs7590912	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7591296	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7591347	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8265	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs917960	0.86[ASN][1000 genomes]
rs917962	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917963	0.81[ASN][1000 genomes]
rs9309042	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs962262	0.85[ASN][1000 genomes]
rs997976	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
5	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
7	chr2:39983000-39999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:39984800-39999600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
10	chr2:39985200-39999600	Weak transcription	Brain Germinal Matrix	brain
11	chr2:39985200-39999600	Weak transcription	Psoas Muscle	Psoas
12	chr2:39985200-39999800	Weak transcription	Brain Substantia Nigra	brain
13	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
15	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:39985800-39999200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:39985800-39999400	Weak transcription	Aorta	Aorta
18	chr2:39985800-39999600	Weak transcription	Brain Angular Gyrus	brain
19	chr2:39985800-39999800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:39985800-39999800	Weak transcription	Small Intestine	intestine
21	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
22	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:39985800-40005400	Weak transcription	Lung	lung
25	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:39986800-39999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:39987400-39999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:39987400-39999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:39987400-39999800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:39987400-39999800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:39987400-40001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:39987400-40001000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:39987600-40001000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:39987600-40003200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:39988000-39999600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:39988000-40004400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:39988200-39999600	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:39991200-40000200	Strong transcription	A549	lung
40	chr2:39992000-39999200	Weak transcription	K562	blood
41	chr2:39992000-39999400	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:39992000-40004400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:39992000-40004600	Weak transcription	Fetal Kidney	kidney
44	chr2:39995400-40000000	Strong transcription	Primary B cells from cord blood	blood
45	chr2:39995400-40000200	Strong transcription	Fetal Thymus	thymus
46	chr2:39995800-39999200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:39995800-39999200	Strong transcription	GM12878-XiMat	blood
48	chr2:39995800-39999800	Strong transcription	Dnd41	blood
49	chr2:39996200-39999600	Weak transcription	Brain Anterior Caudate	brain
50	chr2:39996400-39999400	Weak transcription	Ovary	ovary

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