Variant report

Variant	rs9755640
Chromosome Location	chr3:42841042-42841043
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	chr3:42840530..42842881-chr6:27858992..27861024,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11129971	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11129973	1.00[ASW][hapmap];0.93[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11708224	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11720829	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12488173	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13062528	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs1564176	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564177	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1991438	0.92[AFR][1000 genomes]
rs339663	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339669	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339673	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339675	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339679	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35033264	1.00[MEX][hapmap]
rs35426298	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4399859	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4404423	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682855	0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683331	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683334	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs5027058	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60959614	0.85[AMR][1000 genomes]
rs6442065	0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773636	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773675	1.00[MEX][hapmap]
rs6777653	1.00[MEX][hapmap]
rs6778695	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6802779	1.00[MEX][hapmap]
rs7610350	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]
rs7611520	1.00[AMR][1000 genomes]
rs7612614	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614158	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648688	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9862147	0.85[AMR][1000 genomes]
rs9866005	0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9882356	1.00[MEX][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3504892	chr3:42837523-42841746	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv3461804	chr3:42837918-42841129	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv1004289	chr3:42838111-42841219	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv6998	chr3:42838163-42841083	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	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
6	esv3322809	chr3:42838473-42841321	Weak transcription Genic enhancers ZNF genes & repeats Enhancers Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42815200-42842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:42815200-42842200	Weak transcription	Aorta	Aorta
3	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
4	chr3:42815400-42844000	Weak transcription	NHDF-Ad	bronchial
5	chr3:42815600-42841800	Weak transcription	Thymus	Thymus
6	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:42822000-42841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:42822400-42843400	Weak transcription	Small Intestine	intestine
10	chr3:42822800-42841600	Weak transcription	Brain Substantia Nigra	brain
11	chr3:42822800-42842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:42822800-42844000	Weak transcription	Fetal Kidney	kidney
13	chr3:42822800-42844200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:42823000-42842800	Weak transcription	Fetal Brain Male	brain
15	chr3:42825200-42843800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:42827600-42844600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr3:42828600-42844000	Weak transcription	NH-A	brain
18	chr3:42830400-42844000	Weak transcription	NHEK	skin
19	chr3:42830800-42841800	Weak transcription	Fetal Thymus	thymus
20	chr3:42832800-42842000	Weak transcription	Fetal Heart	heart
21	chr3:42832800-42843800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:42835200-42842200	Weak transcription	Fetal Lung	lung
23	chr3:42835400-42841200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr3:42835400-42841200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:42835400-42841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:42835400-42842400	Weak transcription	Right Ventricle	heart
27	chr3:42835400-42842600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:42835400-42843400	Weak transcription	Colonic Mucosa	Colon
29	chr3:42835400-42843400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:42835400-42843400	Weak transcription	HSMMtube	muscle
31	chr3:42835400-42844000	Weak transcription	Osteobl	bone
32	chr3:42835400-42844200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:42835400-42844200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:42835400-42844200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:42835400-42844200	Weak transcription	Fetal Stomach	stomach
36	chr3:42835400-42844200	Weak transcription	A549	lung
37	chr3:42835400-42844200	Weak transcription	HUVEC	blood vessel
38	chr3:42835400-42844200	Weak transcription	NHLF	lung
39	chr3:42835400-42844400	Weak transcription	Primary B cells from cord blood	blood
40	chr3:42835400-42844600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:42835400-42844600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:42835400-42844600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:42835400-42844600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:42835400-42844600	Weak transcription	Esophagus	oesophagus
45	chr3:42835400-42844600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:42835400-42844600	Weak transcription	Lung	lung
47	chr3:42835400-42844600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:42835400-42844800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:42835400-42844800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:42835400-42844800	Weak transcription	Ovary	ovary

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