Variant report

Variant	rs2241291
Chromosome Location	chr7:127638874-127638875
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:127635606..127639258-chr7:127641258..127643536,3	K562	blood:
2	chr7:127632086..127635094-chr7:127636787..127638892,4	K562	blood:
3	chr7:127637391..127639258-chr7:127640578..127642827,2	K562	blood:
4	chr7:127622847..127627413-chr7:127635236..127639415,6	K562	blood:
5	chr7:127622847..127631238-chr7:127633836..127639415,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LEP-5	chr7:127637562-127640130	NONHSAT123162

No data

Variant related genes	Relation type
ENSG00000197157	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	0.97[AMR][1000 genomes];1.00[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];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1193331	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1193333	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1193335	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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];0.90[AMR][1000 genomes]
rs12539411	0.83[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];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12673293	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1345509	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1419967	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1419968	0.88[JPT][hapmap]
rs16871926	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17151377	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17151470	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2058457	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2543477	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322813	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs322816	0.86[AMR][1000 genomes]
rs322817	0.89[AMR][1000 genomes]
rs322819	0.85[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes]
rs322820	0.81[CHB][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.88[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];0.90[AMR][1000 genomes]
rs322822	0.90[AMR][1000 genomes]
rs322823	0.85[CHB][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs322824	0.90[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];0.90[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	0.90[AMR][1000 genomes]
rs322830	0.90[AMR][1000 genomes]
rs322837	0.90[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];0.87[AMR][1000 genomes]
rs35774036	0.83[ASN][1000 genomes]
rs3757754	0.90[AMR][1000 genomes]
rs3757759	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3757760	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]
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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757771	0.84[AMR][1000 genomes]
rs3757778	0.83[EUR][1000 genomes]
rs3779522	0.90[AMR][1000 genomes]
rs3779523	0.85[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes]
rs3779526	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3779527	0.96[AMR][1000 genomes];0.99[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	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3808086	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[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];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3823995	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3824003	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4728079	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4731389	0.81[ASN][1000 genomes]
rs58106688	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62481416	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62481419	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62481443	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62481447	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62481450	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6467155	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467156	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67338333	0.83[EUR][1000 genomes]
rs6969233	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6972847	0.83[EUR][1000 genomes]
rs6973092	0.94[JPT][hapmap]
rs765971	0.80[AMR][1000 genomes]
rs7789322	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882694	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9791922	0.87[AMR][1000 genomes];0.87[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
rs2241291	GCC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127617600-127640600	Weak transcription	Brain Germinal Matrix	brain
2	chr7:127621000-127643600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:127627200-127644800	Weak transcription	Fetal Brain Female	brain
4	chr7:127628400-127639400	Strong transcription	GM12878-XiMat	blood
5	chr7:127628400-127648400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:127630400-127644000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:127630600-127641400	Strong transcription	Primary T cells from cord blood	blood
8	chr7:127631200-127655600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:127631800-127660800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:127632000-127640600	Weak transcription	Gastric	stomach
11	chr7:127632400-127641000	Weak transcription	Colonic Mucosa	Colon
12	chr7:127632400-127643400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:127632400-127643600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:127632400-127643800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:127632600-127657600	Weak transcription	HUVEC	blood vessel
16	chr7:127632800-127639200	Enhancers	Fetal Heart	heart
17	chr7:127633600-127643600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:127634000-127641000	Weak transcription	Hela-S3	cervix
19	chr7:127634200-127643400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:127634200-127643600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr7:127634200-127657800	Weak transcription	NH-A	brain
22	chr7:127634400-127639400	Weak transcription	Fetal Intestine Large	intestine
23	chr7:127634400-127640600	Weak transcription	Esophagus	oesophagus
24	chr7:127634400-127641400	Weak transcription	NHEK	skin
25	chr7:127634600-127639600	Weak transcription	Fetal Intestine Small	intestine
26	chr7:127634600-127642600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:127634600-127646000	Weak transcription	Thymus	Thymus
28	chr7:127635000-127639000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:127635600-127639200	Enhancers	Fetal Lung	lung
30	chr7:127635600-127640600	Weak transcription	Pancreas	Pancrea
31	chr7:127635600-127642600	Weak transcription	Placenta	Placenta
32	chr7:127635600-127660600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:127635800-127639200	Strong transcription	Fetal Thymus	thymus
34	chr7:127635800-127640800	Enhancers	Adipose Nuclei	Adipose
35	chr7:127635800-127660600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr7:127636000-127640600	Weak transcription	Fetal Kidney	kidney
37	chr7:127636000-127641000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr7:127636000-127646000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:127636000-127662400	Weak transcription	NHDF-Ad	bronchial
40	chr7:127636200-127644800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:127636200-127645200	Weak transcription	Fetal Stomach	stomach
42	chr7:127636200-127646000	Weak transcription	Fetal Brain Male	brain
43	chr7:127636400-127640600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr7:127636400-127643600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr7:127636600-127639000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr7:127636600-127640400	Weak transcription	Lung	lung
47	chr7:127636600-127640600	Weak transcription	Spleen	Spleen
48	chr7:127636600-127640800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:127636600-127643800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:127636600-127650400	Weak transcription	Colon Smooth Muscle	Colon

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