Variant report

Variant	rs7610350
Chromosome Location	chr3:42842245-42842246
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	FOXA1	chr3:42842069-42842418	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:42841822-42846994	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA2	chr3:42842144-42842392	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:42842172-42842933	K562	blood:	n/a	n/a
5	FOXA1	chr3:42842141-42842496	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:42841846-42842345	MCF10A-Er-Src	breast:	n/a	n/a
7	ZNF384	chr3:42841983-42842443	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42841845..42845236-chr3:42855285..42858253,3	K562	blood:
2	chr3:42841907..42845904-chr3:42858547..42863038,5	K562	blood:
3	chr3:42631172..42633792-chr3:42841692..42844503,2	K562	blood:
4	chr3:42840530..42842881-chr6:27858992..27861024,2	MCF-7	breast:

Variant related genes	Relation type
ACKR2	TF binding region
ENSG00000144648	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11129971	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11720829	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12488173	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13062528	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs1564176	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564177	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1991438	0.91[AFR][1000 genomes]
rs339663	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339669	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339679	0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35033264	1.00[MEX][hapmap]
rs35426298	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404423	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683334	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs5027058	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773636	0.95[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773675	1.00[MEX][hapmap]
rs6777653	1.00[MEX][hapmap]
rs6778695	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6802779	1.00[MEX][hapmap]
rs7611520	1.00[AMR][1000 genomes]
rs7612614	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7620291	0.81[AFR][1000 genomes]
rs7648688	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9755640	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9866005	0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	1.00[MEX][hapmap];0.85[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv435763	chr3:42838241-42843142	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
2	chr3:42815400-42844000	Weak transcription	NHDF-Ad	bronchial
3	chr3:42822400-42843400	Weak transcription	Small Intestine	intestine
4	chr3:42822800-42842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:42822800-42844000	Weak transcription	Fetal Kidney	kidney
6	chr3:42822800-42844200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:42823000-42842800	Weak transcription	Fetal Brain Male	brain
8	chr3:42825200-42843800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:42827600-42844600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:42828600-42844000	Weak transcription	NH-A	brain
11	chr3:42830400-42844000	Weak transcription	NHEK	skin
12	chr3:42832800-42843800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:42835400-42842400	Weak transcription	Right Ventricle	heart
14	chr3:42835400-42842600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:42835400-42843400	Weak transcription	Colonic Mucosa	Colon
16	chr3:42835400-42843400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:42835400-42843400	Weak transcription	HSMMtube	muscle
18	chr3:42835400-42844000	Weak transcription	Osteobl	bone
19	chr3:42835400-42844200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:42835400-42844200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:42835400-42844200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:42835400-42844200	Weak transcription	Fetal Stomach	stomach
23	chr3:42835400-42844200	Weak transcription	A549	lung
24	chr3:42835400-42844200	Weak transcription	HUVEC	blood vessel
25	chr3:42835400-42844200	Weak transcription	NHLF	lung
26	chr3:42835400-42844400	Weak transcription	Primary B cells from cord blood	blood
27	chr3:42835400-42844600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:42835400-42844600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:42835400-42844600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:42835400-42844600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:42835400-42844600	Weak transcription	Esophagus	oesophagus
32	chr3:42835400-42844600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:42835400-42844600	Weak transcription	Lung	lung
34	chr3:42835400-42844600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:42835400-42844800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:42835400-42844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:42835400-42844800	Weak transcription	Ovary	ovary
38	chr3:42835600-42842600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:42835600-42842800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:42835600-42843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:42835600-42843200	Weak transcription	Fetal Brain Female	brain
42	chr3:42835600-42843400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:42835600-42844200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:42835600-42844200	Weak transcription	Placenta	Placenta
45	chr3:42835800-42842600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:42835800-42843400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:42835800-42843400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:42835800-42844000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:42835800-42844200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:42835800-42844600	Weak transcription	Primary hematopoietic stem cells	blood

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