Variant report

Variant	rs6707728
Chromosome Location	chr2:231260654-231260655
allele	G/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	chr2:231260166-231260795	K562	blood:	n/a	n/a

Variant related genes	Relation type
SP140L	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10933334	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10933336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688808	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11902383	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12104570	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12694857	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1582830	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1820550	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1968340	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1968341	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1974984	0.81[ASN][1000 genomes]
rs3845827	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6436929	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6436932	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6436935	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6717687	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6728619	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6731825	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737808	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6741595	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6742975	0.98[EUR][1000 genomes]
rs6746556	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563493	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7607380	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3486129	chr2:231175581-231265831	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3486131	chr2:231175581-231265831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231212800-231262400	Weak transcription	K562	blood
2	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
3	chr2:231222200-231273200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:231223600-231263600	Weak transcription	Fetal Kidney	kidney
5	chr2:231225200-231268000	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:231228800-231275600	Weak transcription	Psoas Muscle	Psoas
7	chr2:231234200-231274400	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:231237000-231264800	Weak transcription	HepG2	liver
9	chr2:231237200-231264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:231245200-231265600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:231245800-231266000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:231248000-231262600	Strong transcription	Liver	Liver
13	chr2:231248000-231265400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:231248000-231274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:231248400-231260800	Strong transcription	Dnd41	blood
16	chr2:231249000-231262000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:231249000-231273200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:231249200-231261800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:231249200-231262000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:231249400-231262000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr2:231249800-231262600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:231250200-231273200	Weak transcription	Right Ventricle	heart
23	chr2:231251600-231261400	Strong transcription	HSMM	muscle
24	chr2:231252000-231261400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:231252600-231272600	Weak transcription	NHDF-Ad	bronchial
26	chr2:231253400-231262600	Strong transcription	Lung	lung
27	chr2:231253600-231262200	Strong transcription	Left Ventricle	heart
28	chr2:231253600-231265800	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:231254000-231264800	Weak transcription	Colonic Mucosa	Colon
30	chr2:231254200-231272800	Weak transcription	NHEK	skin
31	chr2:231254400-231264800	Weak transcription	Gastric	stomach
32	chr2:231254400-231265000	Weak transcription	Pancreas	Pancrea
33	chr2:231254400-231267800	Weak transcription	NHLF	lung
34	chr2:231255200-231275600	Weak transcription	HMEC	breast
35	chr2:231256200-231265000	Weak transcription	HUVEC	blood vessel
36	chr2:231258000-231267600	Weak transcription	Esophagus	oesophagus
37	chr2:231258200-231273000	Weak transcription	NH-A	brain
38	chr2:231258600-231265400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr2:231258800-231261000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr2:231258800-231261400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:231258800-231275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:231259200-231261000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
43	chr2:231259200-231261800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:231259200-231262200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:231259200-231262200	Strong transcription	Osteobl	bone
46	chr2:231259400-231261000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr2:231259400-231261200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
48	chr2:231259400-231261400	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr2:231259400-231261800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:231259600-231261200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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