Variant report

Variant	rs3757760
Chromosome Location	chr7:127658196-127658197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127657760..127658313-chr7:127849422..127849977,2	MCF-7	breast:
2	chr7:127657571..127659586-chr7:127661972..127664018,2	K562	blood:
3	chr7:127651063..127656520-chr7:127658090..127661426,7	K562	blood:
4	chr7:127648714..127651621-chr7:127657028..127659226,2	MCF-7	breast:
5	chr7:127646218..127648423-chr7:127655785..127658353,2	K562	blood:
6	chr7:127658157..127661100-chr7:127671141..127673434,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128594	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1024910	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10954164	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11768841	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1193331	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1193333	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193335	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193336	0.84[ASN][1000 genomes]
rs124756	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs12539411	0.82[EUR][1000 genomes]
rs12668077	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12673293	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1345509	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1419967	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1419968	0.88[JPT][hapmap]
rs16871926	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17151377	0.82[EUR][1000 genomes]
rs17151470	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2058457	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2543477	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322781	0.81[AMR][1000 genomes]
rs322813	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs322816	0.88[AMR][1000 genomes]
rs322817	0.88[AMR][1000 genomes]
rs322819	0.85[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs322820	0.81[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs322821	0.82[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs322822	0.89[AMR][1000 genomes]
rs322823	0.85[CHB][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes]
rs322824	0.89[AMR][1000 genomes]
rs322825	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs322826	0.80[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap]
rs322827	0.88[JPT][hapmap]
rs322828	0.88[JPT][hapmap]
rs322829	0.89[AMR][1000 genomes]
rs322830	0.89[AMR][1000 genomes]
rs322837	0.89[AMR][1000 genomes]
rs322840	0.82[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs35774036	0.83[ASN][1000 genomes]
rs3757754	0.89[AMR][1000 genomes]
rs3757759	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3757763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757771	0.83[AMR][1000 genomes]
rs3757778	0.82[EUR][1000 genomes]
rs3779522	0.89[AMR][1000 genomes]
rs3779523	0.85[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes]
rs3779526	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3779527	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3808056	0.88[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs3808077	0.81[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3808078	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808086	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3808088	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3823995	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3824003	0.82[EUR][1000 genomes]
rs4728079	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4731389	0.81[ASN][1000 genomes]
rs58106688	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62481416	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62481419	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62481443	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62481447	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62481450	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6467155	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467156	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67338333	0.82[EUR][1000 genomes]
rs6969233	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6972847	0.83[EUR][1000 genomes]
rs6973092	0.94[JPT][hapmap]
rs7789322	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882694	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9791922	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1024743	chr7:127498695-127670004	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3757760	GCC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127631800-127660800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:127635600-127660600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:127635800-127660600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:127636000-127662400	Weak transcription	NHDF-Ad	bronchial
5	chr7:127637000-127658800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:127641600-127670400	Weak transcription	Colonic Mucosa	Colon
7	chr7:127644000-127660200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:127644000-127668800	Weak transcription	Dnd41	blood
9	chr7:127644000-127670200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr7:127644800-127667400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr7:127644800-127670800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:127645000-127684000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:127645200-127661800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:127645400-127670000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:127646000-127660400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:127650000-127659800	Strong transcription	K562	blood
17	chr7:127651600-127659800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:127651800-127659600	Strong transcription	HepG2	liver
19	chr7:127651800-127660600	Weak transcription	Left Ventricle	heart
20	chr7:127651800-127661600	Strong transcription	Fetal Intestine Small	intestine
21	chr7:127651800-127664400	Weak transcription	Right Ventricle	heart
22	chr7:127651800-127665600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr7:127651800-127667600	Weak transcription	Colon Smooth Muscle	Colon
24	chr7:127651800-127668800	Weak transcription	Ovary	ovary
25	chr7:127651800-127670600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr7:127652000-127660600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:127652600-127659000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:127653000-127658600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:127653000-127658600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr7:127653000-127661000	Weak transcription	A549	lung
31	chr7:127653200-127658800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr7:127653200-127659000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:127653200-127668800	Weak transcription	Thymus	Thymus
34	chr7:127653400-127661200	Weak transcription	NHLF	lung
35	chr7:127653400-127662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:127653600-127660600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:127654600-127660600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:127654600-127669200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:127654800-127664200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr7:127655200-127660000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr7:127655400-127658200	Weak transcription	Right Atrium	heart
42	chr7:127655600-127659000	Weak transcription	Fetal Brain Male	brain
43	chr7:127656000-127658200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:127656600-127658600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr7:127656600-127658800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:127656600-127660000	Strong transcription	NHEK	skin
47	chr7:127656600-127660400	Enhancers	Brain Anterior Caudate	brain
48	chr7:127656600-127662200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr7:127656800-127658200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr7:127656800-127658800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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