Variant report

Variant	rs4670956
Chromosome Location	chr2:39974442-39974443
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	POLR2A	chr2:39974051-39975112	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39969831..39971632-chr2:39972593..39975099,2	MCF-7	breast:
2	chr2:39967992..39971094-chr2:39972706..39975248,3	K562	blood:

Variant related genes	Relation type
THUMPD2	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10174709	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10206408	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10207589	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs10211306	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1035138	0.83[ASN][1000 genomes]
rs1035139	0.83[ASN][1000 genomes]
rs11124691	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11124693	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs11684302	0.81[CEU][hapmap]
rs12470473	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617624	0.87[ASN][1000 genomes]
rs12623462	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12623545	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12624217	0.80[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12712653	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12712656	0.80[CEU][hapmap]
rs13026313	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13425906	0.86[ASN][1000 genomes]
rs1548877	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1861243	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1861258	0.83[CEU][hapmap]
rs1986876	0.81[CEU][hapmap];0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs2041735	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2058620	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2110656	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160198	0.83[CHB][hapmap]
rs2241115	0.84[JPT][hapmap]
rs2373688	0.81[ASN][1000 genomes]
rs2373689	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2540226	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2540227	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2540228	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2716704	0.83[ASN][1000 genomes]
rs2716727	0.85[ASN][1000 genomes]
rs2716729	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2716730	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35761077	0.81[ASN][1000 genomes]
rs3732121	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732122	0.93[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670955	0.86[ASN][1000 genomes]
rs4670957	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4670958	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4670959	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs59756273	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544242	0.93[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6719179	0.84[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6722610	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6731026	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747842	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6750252	0.92[ASN][1000 genomes]
rs6758453	0.93[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs727376	0.83[ASN][1000 genomes]
rs7560642	0.88[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7565954	0.93[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7581406	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7590912	0.86[EUR][1000 genomes]
rs7591296	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7591347	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8265	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs917960	0.87[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs917962	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917963	0.81[CEU][hapmap];0.94[CHB][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309042	0.82[ASN][1000 genomes]
rs962262	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs997976	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39944400-39976600	Weak transcription	Fetal Brain Male	brain
2	chr2:39960200-39987200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:39960400-39983000	Weak transcription	Stomach Mucosa	stomach
4	chr2:39961200-39974600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:39961400-39984200	Weak transcription	Colonic Mucosa	Colon
6	chr2:39962200-39986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:39962200-39993200	Strong transcription	Liver	Liver
8	chr2:39962800-39980200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:39963200-39982000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:39964000-39976800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:39964200-39976800	Weak transcription	Brain Substantia Nigra	brain
12	chr2:39964200-39977000	Weak transcription	Brain Angular Gyrus	brain
13	chr2:39964200-39977400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:39964200-39984200	Weak transcription	Psoas Muscle	Psoas
15	chr2:39964400-39977000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:39964800-39983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:39965200-39976600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:39965200-39980000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:39965200-39983000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:39965400-39984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:39965600-39975400	Weak transcription	Fetal Kidney	kidney
24	chr2:39966600-39976800	Weak transcription	Small Intestine	intestine
25	chr2:39966800-39975800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:39966800-39980000	Weak transcription	Esophagus	oesophagus
27	chr2:39966800-39980200	Weak transcription	Lung	lung
28	chr2:39966800-39983200	Weak transcription	Spleen	Spleen
29	chr2:39967000-39976200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:39967000-39976800	Weak transcription	Gastric	stomach
31	chr2:39967000-39981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:39967000-39983000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:39967000-39983200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:39967000-39983400	Weak transcription	Aorta	Aorta
35	chr2:39967200-39976600	Weak transcription	Brain Germinal Matrix	brain
36	chr2:39967200-39983000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:39967600-39976800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr2:39967600-39991200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:39967800-39976400	Weak transcription	Brain Anterior Caudate	brain
40	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:39970000-39975200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:39970000-39975400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:39970000-39976800	Weak transcription	HSMMtube	muscle
44	chr2:39970200-39978200	Weak transcription	GM12878-XiMat	blood
45	chr2:39970600-39976200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr2:39970800-39976800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:39970800-39983000	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:39971000-39975200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:39971000-39975800	Weak transcription	Fetal Brain Female	brain
50	chr2:39971000-39976000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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