Variant report

Variant	rs1541711
Chromosome Location	chr7:129029391-129029392
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	chr7:129028946..129033596-chr7:129035556..129037411,4	K562	blood:
2	chr7:129028946..129031606-chr7:129035556..129037411,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1000676	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10248810	0.86[JPT][hapmap]
rs10954226	0.86[JPT][hapmap]
rs10954228	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10954229	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10954230	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10954231	0.85[ASN][1000 genomes]
rs11979476	0.86[JPT][hapmap]
rs12112374	0.86[JPT][hapmap]
rs12534372	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12540568	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12667132	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12667232	0.84[TSI][hapmap]
rs12668958	1.00[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs12671604	0.84[TSI][hapmap]
rs1526900	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs1559486	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs17168734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17168750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1880854	0.86[JPT][hapmap]
rs2694572	0.86[JPT][hapmap]
rs2694574	0.84[JPT][hapmap]
rs2718083	0.80[JPT][hapmap]
rs2718084	0.81[JPT][hapmap]
rs34022136	0.96[ASN][1000 genomes]
rs35305688	0.84[ASN][1000 genomes]
rs35366945	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35974655	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4460315	0.82[ASN][1000 genomes]
rs4728162	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4728163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728164	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4731572	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731573	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4731575	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6467233	0.81[JPT][hapmap]
rs6966595	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs6980385	0.86[JPT][hapmap]
rs753336	0.84[TSI][hapmap]
rs7788327	0.86[JPT][hapmap]
rs822038	0.90[CHD][hapmap];0.91[JPT][hapmap]
rs822040	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs891545	0.81[JPT][hapmap]
rs963465	0.81[JPT][hapmap]
rs9641846	0.81[JPT][hapmap]
rs9641850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641851	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs966481	0.84[TSI][hapmap]
rs974558	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1541711	AHCYL2	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128989200-129044200	Weak transcription	Ovary	ovary
2	chr7:129006200-129046000	Weak transcription	Aorta	Aorta
3	chr7:129008200-129035000	Weak transcription	Psoas Muscle	Psoas
4	chr7:129008400-129044200	Weak transcription	Fetal Muscle Leg	muscle
5	chr7:129008400-129073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:129008600-129037200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:129008800-129035000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr7:129008800-129035000	Weak transcription	Fetal Stomach	stomach
9	chr7:129008800-129035200	Weak transcription	Lung	lung
10	chr7:129008800-129039800	Weak transcription	Placenta	Placenta
11	chr7:129010400-129041000	Weak transcription	Esophagus	oesophagus
12	chr7:129011400-129030400	Weak transcription	Fetal Intestine Small	intestine
13	chr7:129015200-129029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr7:129015800-129053400	Weak transcription	Fetal Lung	lung
15	chr7:129016000-129029400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:129016000-129062400	Weak transcription	Pancreas	Pancrea
17	chr7:129016000-129071400	Weak transcription	Small Intestine	intestine
18	chr7:129016400-129052400	Weak transcription	Fetal Kidney	kidney
19	chr7:129016600-129035000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:129016600-129055200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:129017400-129030000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:129017400-129030400	Weak transcription	Colonic Mucosa	Colon
23	chr7:129017400-129035000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:129017400-129041000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:129017400-129051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr7:129017400-129069200	Weak transcription	Stomach Mucosa	stomach
27	chr7:129017400-129073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:129017600-129036800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:129017600-129036800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:129017600-129041000	Weak transcription	Hela-S3	cervix
31	chr7:129017600-129041000	Weak transcription	HMEC	breast
32	chr7:129017800-129037000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:129017800-129064600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr7:129018400-129035000	Weak transcription	Gastric	stomach
35	chr7:129018400-129070000	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:129019400-129070800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:129019600-129034000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr7:129019800-129066200	Weak transcription	Thymus	Thymus
39	chr7:129020000-129064600	Weak transcription	Spleen	Spleen
40	chr7:129020200-129029400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr7:129020200-129035000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:129020400-129035000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:129020600-129029400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr7:129020600-129029400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:129020600-129029600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr7:129021400-129029600	Weak transcription	Adipose Nuclei	Adipose
47	chr7:129022000-129031200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr7:129022000-129041200	Weak transcription	GM12878-XiMat	blood
49	chr7:129023000-129030400	Weak transcription	HSMMtube	muscle
50	chr7:129023000-129047800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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