Variant report

Variant	rs6753987
Chromosome Location	chr2:97521820-97521821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
2	chr2:97481330..97483685-chr2:97521136..97525158,3	K562	blood:
3	chr2:97480014..97482644-chr2:97518894..97524629,5	MCF-7	breast:
4	chr2:97502679..97504897-chr2:97518482..97522154,3	MCF-7	breast:
5	chr2:97481330..97485256-chr2:97521136..97525640,5	K562	blood:
6	chr2:97521500..97526453-chr2:97614513..97620136,8	K562	blood:
7	chr2:97521500..97526547-chr2:97614513..97619168,8	K562	blood:

Variant related genes	Relation type
ENSG00000168763	Chromatin interaction
ENSG00000252845	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10203346	0.96[EUR][1000 genomes]
rs10439526	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11897786	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12172	0.93[EUR][1000 genomes]
rs1317911	0.83[AMR][1000 genomes]
rs1320146	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1320149	0.83[AMR][1000 genomes]
rs13419073	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17119562	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17119564	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs17119591	1.00[CHB][hapmap]
rs17119598	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2139406	1.00[GIH][hapmap]
rs2276654	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2280356	1.00[GIH][hapmap]
rs2872633	1.00[GIH][hapmap]
rs3731940	1.00[GIH][hapmap]
rs3731941	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs4077343	0.81[EUR][1000 genomes]
rs58147284	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59244622	0.93[EUR][1000 genomes]
rs62152790	0.81[EUR][1000 genomes]
rs62152793	0.84[EUR][1000 genomes]
rs62152794	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62152834	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62152860	0.96[EUR][1000 genomes]
rs62152863	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152864	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576986	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6576987	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6576989	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6751132	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6756482	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6758151	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs72811623	0.95[EUR][1000 genomes]
rs72811627	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72811629	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580942	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs7594727	1.00[MEX][hapmap];0.88[TSI][hapmap]
rs7608621	1.00[MEX][hapmap];0.82[TSI][hapmap]
rs9948	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs9973492	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1009720	chr2:97464803-97522856	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv535830	chr2:97464803-97522856	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97499200-97522400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:97499600-97522800	Weak transcription	HSMM	muscle
3	chr2:97503600-97522600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:97505600-97522400	Weak transcription	NH-A	brain
5	chr2:97505800-97522400	Weak transcription	Stomach Mucosa	stomach
6	chr2:97510600-97522600	Weak transcription	Right Atrium	heart
7	chr2:97514000-97522400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:97514800-97522800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:97515400-97522400	Weak transcription	NHDF-Ad	bronchial
10	chr2:97517600-97522400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:97517600-97522400	Weak transcription	Fetal Kidney	kidney
12	chr2:97517600-97522400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:97517600-97522400	Weak transcription	Small Intestine	intestine
14	chr2:97517800-97522000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:97518600-97522800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:97518800-97522400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:97518800-97522400	Weak transcription	Psoas Muscle	Psoas
18	chr2:97518800-97522400	Weak transcription	HUVEC	blood vessel
19	chr2:97519400-97522000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:97519400-97522000	Weak transcription	Primary B cells from cord blood	blood
21	chr2:97519400-97522400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:97519400-97522400	Weak transcription	Fetal Lung	lung
23	chr2:97519400-97522400	Weak transcription	HSMMtube	muscle
24	chr2:97519400-97522600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:97519400-97522600	Weak transcription	Colonic Mucosa	Colon
26	chr2:97519400-97522600	Weak transcription	Gastric	stomach
27	chr2:97519400-97522800	Weak transcription	Lung	lung
28	chr2:97519600-97522000	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:97519600-97522000	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:97519600-97522200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:97519600-97522200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:97519600-97522200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:97519600-97522200	Weak transcription	Brain Germinal Matrix	brain
34	chr2:97519600-97522200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:97519600-97522200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:97519600-97522200	Weak transcription	A549	lung
37	chr2:97519600-97522200	Weak transcription	NHLF	lung
38	chr2:97519600-97522400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:97519600-97522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:97519600-97522400	Weak transcription	Ovary	ovary
41	chr2:97519600-97522400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:97519600-97522600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:97519600-97522600	Weak transcription	Right Ventricle	heart
44	chr2:97519800-97522400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:97520000-97522400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:97520200-97522000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:97520200-97522000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:97520200-97522000	Weak transcription	Fetal Intestine Small	intestine
49	chr2:97520200-97522000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr2:97520200-97522200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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