Variant report

Variant	rs3002297
Chromosome Location	chr1:214536061-214536062
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:214533625..214536259-chr1:214538057..214540162,2	MCF-7	breast:
2	chr1:214528682..214531608-chr1:214533975..214536606,2	K562	blood:

Variant related genes	Relation type
ENSG00000228470	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10735513	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10779613	0.86[CHB][hapmap]
rs10864092	0.86[CHB][hapmap]
rs11120292	0.86[CHB][hapmap]
rs11120295	0.86[CHB][hapmap]
rs11120309	0.81[CHB][hapmap]
rs1134647	0.86[CHB][hapmap]
rs1135352	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11587662	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12124666	0.86[CHB][hapmap]
rs12137369	0.86[ASN][1000 genomes]
rs1472439	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1472443	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270704	0.86[CHB][hapmap]
rs2291829	0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2291830	0.86[CHB][hapmap]
rs2936014	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2936015	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2936016	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2936017	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2936018	0.81[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3002298	0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3002299	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002300	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002301	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002303	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002305	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3002306	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3002307	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3002308	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3002309	0.94[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3002312	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3013442	0.82[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3013446	0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3013448	0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3013451	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3013452	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3013455	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4129186	0.81[CHB][hapmap]
rs4578186	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4655245	0.86[CHB][hapmap]
rs4655248	0.81[ASN][1000 genomes]
rs4655335	0.86[CHB][hapmap]
rs4655342	0.82[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6540817	0.86[CHB][hapmap]
rs6540819	0.86[CHB][hapmap]
rs6540821	0.86[CHB][hapmap]
rs6540822	0.86[CHB][hapmap]
rs6657368	0.82[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs6662864	0.86[CHB][hapmap]
rs6665343	0.86[CHB][hapmap]
rs6670349	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6687411	0.85[CHB][hapmap]
rs6691083	0.86[CHB][hapmap]
rs6700976	0.86[CHB][hapmap]
rs6701764	0.86[CHB][hapmap]
rs7413877	0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7419021	0.86[CHB][hapmap]
rs7512745	0.86[CHB][hapmap]
rs7530350	0.81[CHB][hapmap]
rs7550799	0.82[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9429918	0.85[CHB][hapmap]

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	esv3323745	chr1:214535996-214536257	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214503200-214537800	Weak transcription	Gastric	stomach
2	chr1:214512000-214537000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:214513600-214552200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:214514000-214537800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:214515400-214542600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:214518400-214537800	Weak transcription	Fetal Brain Male	brain
7	chr1:214519000-214557800	Weak transcription	Dnd41	blood
8	chr1:214519200-214577200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:214521200-214537600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:214522800-214552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:214523400-214540800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:214524400-214574400	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:214524800-214537800	Strong transcription	NHEK	skin
14	chr1:214524800-214539200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:214525000-214537000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:214525600-214540000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:214526000-214538600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:214526000-214544600	Weak transcription	Spleen	Spleen
19	chr1:214526400-214537200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:214526400-214542400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:214527400-214540600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:214527800-214542400	Weak transcription	HepG2	liver
23	chr1:214528600-214539800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:214528600-214552800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:214528600-214555800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:214528800-214537200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:214528800-214538800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:214528800-214539200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:214528800-214551800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:214529000-214538400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:214529000-214584200	Weak transcription	Brain Anterior Caudate	brain
32	chr1:214529200-214539600	Strong transcription	Fetal Stomach	stomach
33	chr1:214529400-214537000	Weak transcription	Fetal Kidney	kidney
34	chr1:214529400-214561800	Weak transcription	Brain Angular Gyrus	brain
35	chr1:214529600-214537800	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr1:214529600-214544600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:214531600-214537000	Weak transcription	Hela-S3	cervix
38	chr1:214531600-214543400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:214531600-214556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:214532000-214537000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:214532000-214537200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:214533000-214539200	Strong transcription	Fetal Lung	lung
43	chr1:214533200-214538400	Strong transcription	NHLF	lung
44	chr1:214533200-214538600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:214533400-214538800	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr1:214533600-214538600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:214533800-214537000	Weak transcription	Ovary	ovary
48	chr1:214534000-214536400	Enhancers	Right Ventricle	heart
49	chr1:214534000-214538800	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr1:214534000-214557000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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