Variant report

Variant	rs6942490
Chromosome Location	chr7:129244793-129244794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:129225250..129227766-chr7:129244638..129247298,2	MCF-7	breast:
2	chr7:129140962..129143945-chr7:129243314..129247330,3	MCF-7	breast:
3	chr7:129244786..129248579-chr7:129273930..129277174,4	MCF-7	breast:
4	chr7:129217261..129219089-chr7:129244632..129246610,2	MCF-7	breast:
5	chr7:129142735..129144736-chr7:129243609..129245473,3	K562	blood:
6	chr7:129244640..129247034-chr7:129428547..129431253,2	K562	blood:
7	chr7:129234956..129236519-chr7:129244483..129247189,2	K562	blood:
8	chr7:129237193..129242343-chr7:129243851..129248345,9	K562	blood:
9	chr7:129228621..129230780-chr7:129244504..129247498,2	K562	blood:
10	chr7:129239952..129242205-chr7:129243025..129245366,3	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBE2H-2	chr7:129242678-129251482	NONHSAT123298
2	lnc-UBE2H-2	chr7:129244389-129251471	ENSG00000273329.1

No data

Variant related genes	Relation type
ENSG00000240204	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10224702	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10231985	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10234904	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs10245818	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10256014	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10258498	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10274906	0.80[ASN][1000 genomes]
rs10276606	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap]
rs10279678	0.80[ASN][1000 genomes]
rs11487138	0.84[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs2402964	0.93[CHD][hapmap];0.87[JPT][hapmap]
rs28689822	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28889902	0.96[EUR][1000 genomes]
rs55933630	0.96[EUR][1000 genomes]
rs56028831	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56271323	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56889501	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62489268	0.80[ASN][1000 genomes]
rs6953077	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs6961403	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs6969098	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6976507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979455	0.82[ASN][1000 genomes]
rs73159612	0.85[ASN][1000 genomes]
rs753947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7777812	0.87[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap]
rs7782066	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7795187	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7796553	0.84[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap]
rs7797729	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs7800226	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7808752	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6942490	OPN1SW	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129232600-129246000	Weak transcription	HMEC	breast
2	chr7:129232600-129246800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:129233400-129246600	Weak transcription	NHEK	skin
4	chr7:129233400-129247400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:129233600-129246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:129233800-129246400	Weak transcription	Placenta	Placenta
7	chr7:129235200-129249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:129235200-129249800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:129235200-129250200	Weak transcription	Right Atrium	heart
10	chr7:129235400-129245800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:129236000-129245800	Weak transcription	A549	lung
12	chr7:129236000-129249000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:129237000-129246400	Weak transcription	HSMM	muscle
14	chr7:129237000-129248800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:129237000-129249800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:129238200-129248200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:129238800-129250400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:129240200-129250400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:129241400-129247200	Weak transcription	Fetal Thymus	thymus
20	chr7:129242600-129246400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:129242800-129250400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:129243000-129246600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:129243000-129248200	Weak transcription	Fetal Kidney	kidney
24	chr7:129243200-129246600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:129243400-129245800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:129243800-129250200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:129244200-129246600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:129244400-129246600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:129244400-129246600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:129244400-129246600	Weak transcription	Fetal Stomach	stomach
31	chr7:129244400-129246600	Weak transcription	K562	blood
32	chr7:129244600-129244800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr7:129244600-129245200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr7:129244600-129246400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:129244600-129246600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:129244600-129248400	Weak transcription	Fetal Lung	lung
37	chr7:129244600-129249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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