Variant report

Variant	rs11961342
Chromosome Location	chr6:56579348-56579349
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56572377..56575419-chr6:56576421..56579962,3	MCF-7	breast:
2	chr6:56578404..56582346-chr6:56590205..56594810,5	MCF-7	breast:
3	chr6:56567530..56570297-chr6:56577353..56579502,2	MCF-7	breast:
4	chr6:56578880..56580854-chr6:56591144..56593853,2	MCF-7	breast:

Extended variants
information (count: 176 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10498811	0.85[EUR][1000 genomes]
rs10498812	0.81[CEU][hapmap]
rs10498813	0.81[CEU][hapmap]
rs11961141	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11966986	1.00[ASN][1000 genomes]
rs11967796	1.00[ASN][1000 genomes]
rs11968575	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970410	0.90[ASN][1000 genomes]
rs11970648	0.89[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13190784	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13191164	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192037	0.85[EUR][1000 genomes]
rs13192478	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13194625	0.81[CEU][hapmap]
rs13194904	0.81[CEU][hapmap]
rs13196211	0.83[EUR][1000 genomes]
rs13198399	0.98[EUR][1000 genomes]
rs13198938	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200166	0.81[CEU][hapmap]
rs13203000	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs13203681	0.81[CEU][hapmap]
rs13204466	0.81[CEU][hapmap]
rs13205013	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205667	0.81[CEU][hapmap]
rs13206849	0.85[EUR][1000 genomes]
rs13207768	0.81[CEU][hapmap]
rs13210876	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs13218913	0.81[CEU][hapmap]
rs13219546	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13219942	1.00[EUR][1000 genomes]
rs13220618	0.81[CEU][hapmap]
rs13220628	0.86[CEU][hapmap]
rs16888085	0.90[ASN][1000 genomes]
rs16888096	1.00[ASN][1000 genomes]
rs16888106	1.00[ASN][1000 genomes]
rs16888118	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888124	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888126	0.82[EUR][1000 genomes]
rs16888128	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888130	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888133	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888135	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888171	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs17684511	0.85[EUR][1000 genomes]
rs17684553	0.86[EUR][1000 genomes]
rs17684571	0.86[EUR][1000 genomes]
rs17684748	0.81[CEU][hapmap]
rs17684772	0.81[CEU][hapmap]
rs17684784	0.81[CEU][hapmap]
rs17684802	0.81[CEU][hapmap]
rs17684878	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs17684884	0.81[CEU][hapmap]
rs17751682	0.85[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs17751695	0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs17751977	0.81[CEU][hapmap]
rs17752046	0.81[CEU][hapmap]
rs17752106	0.81[CEU][hapmap]
rs1903332	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2144407	1.00[ASN][1000 genomes]
rs2180148	1.00[ASN][1000 genomes]
rs2967960	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3002003	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002007	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3002008	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002009	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002010	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002011	1.00[CEU][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34138864	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34429594	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34455199	0.97[EUR][1000 genomes]
rs34463732	0.90[EUR][1000 genomes]
rs34465210	0.97[EUR][1000 genomes]
rs34566275	0.97[EUR][1000 genomes]
rs34576803	0.83[EUR][1000 genomes]
rs34587484	0.97[EUR][1000 genomes]
rs34623351	0.97[EUR][1000 genomes]
rs34703847	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34724718	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34803237	0.97[EUR][1000 genomes]
rs34812826	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.97[EUR][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35326806	1.00[EUR][1000 genomes]
rs35408048	0.85[EUR][1000 genomes]
rs35494794	1.00[EUR][1000 genomes]
rs35619924	0.85[EUR][1000 genomes]
rs35637749	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35668437	0.85[EUR][1000 genomes]
rs35687635	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35876418	0.97[EUR][1000 genomes]
rs35920751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072271	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073960	0.91[AFR][1000 genomes]
rs4074101	0.85[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4074102	0.85[EUR][1000 genomes]
rs4074103	0.82[EUR][1000 genomes]
rs41267673	1.00[ASN][1000 genomes]
rs41267675	0.97[EUR][1000 genomes]
rs4133076	1.00[ASN][1000 genomes]
rs4275049	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4299824	0.81[CEU][hapmap]
rs4348308	0.81[CEU][hapmap]
rs4371846	0.81[CEU][hapmap]
rs4415160	0.81[CEU][hapmap]
rs4457154	0.81[CEU][hapmap]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5024547	0.85[EUR][1000 genomes]
rs55742092	0.85[EUR][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56101897	0.85[EUR][1000 genomes]
rs56196625	1.00[ASN][1000 genomes]
rs57289287	1.00[ASN][1000 genomes]
rs57392123	1.00[ASN][1000 genomes]
rs57488435	1.00[ASN][1000 genomes]
rs58565063	1.00[ASN][1000 genomes]
rs59073430	1.00[ASN][1000 genomes]
rs59085778	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59772940	1.00[ASN][1000 genomes]
rs59889120	1.00[ASN][1000 genomes]
rs60360551	1.00[ASN][1000 genomes]
rs60498201	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62412526	0.85[EUR][1000 genomes]
rs62412528	0.85[EUR][1000 genomes]
rs62412531	0.85[EUR][1000 genomes]
rs62412532	0.85[EUR][1000 genomes]
rs62412544	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62412556	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6459167	1.00[ASN][1000 genomes]
rs6459168	1.00[ASN][1000 genomes]
rs6900572	1.00[ASN][1000 genomes]
rs6901176	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903815	1.00[ASN][1000 genomes]
rs6904535	0.82[AMR][1000 genomes]
rs6905603	0.81[CEU][hapmap]
rs6916813	1.00[ASN][1000 genomes]
rs6918949	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs6924375	0.86[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926134	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6934714	0.81[CEU][hapmap]
rs6938003	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564848	0.83[EUR][1000 genomes]
rs71564849	0.86[EUR][1000 genomes]
rs73746926	1.00[ASN][1000 genomes]
rs73746929	1.00[ASN][1000 genomes]
rs73746930	1.00[ASN][1000 genomes]
rs73746931	1.00[ASN][1000 genomes]
rs7749100	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7758867	0.81[CEU][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs7759479	1.00[ASN][1000 genomes]
rs7760503	1.00[ASN][1000 genomes]
rs7760542	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7761027	1.00[ASN][1000 genomes]
rs7761501	0.81[CEU][hapmap]
rs7761729	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs7767128	0.83[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771085	0.80[CEU][hapmap]
rs7775134	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11961342	GCM1	cis	parietal	SCAN
rs11961342	BMP5	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
2	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:56568000-56580400	Weak transcription	Brain Germinal Matrix	brain
4	chr6:56570000-56585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
6	chr6:56572400-56579400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:56574800-56579800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:56574800-56580000	Weak transcription	Pancreas	Pancrea
9	chr6:56577200-56580800	Enhancers	Stomach Mucosa	stomach
10	chr6:56577200-56581200	Enhancers	HMEC	breast
11	chr6:56577200-56581400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:56577200-56581600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:56577400-56580000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:56577600-56579400	Enhancers	HSMMtube	muscle
15	chr6:56577600-56579400	Enhancers	Osteobl	bone
16	chr6:56577600-56579600	Enhancers	HUVEC	blood vessel
17	chr6:56577600-56580800	Enhancers	NHEK	skin
18	chr6:56577600-56581000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:56577600-56581400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:56577600-56581400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:56577600-56583000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:56577800-56579600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:56577800-56579600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:56577800-56580000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:56577800-56580000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr6:56577800-56580200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:56577800-56580800	Enhancers	H9 Cell Line	embryonic stem cell
28	chr6:56577800-56580800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:56577800-56580800	Enhancers	Stomach Smooth Muscle	stomach
30	chr6:56577800-56581000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:56577800-56581000	Enhancers	Liver	Liver
32	chr6:56577800-56581000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr6:56577800-56581200	Enhancers	Fetal Heart	heart
34	chr6:56577800-56581200	Enhancers	HepG2	liver
35	chr6:56577800-56581400	Enhancers	Brain Angular Gyrus	brain
36	chr6:56577800-56581400	Enhancers	Colon Smooth Muscle	Colon
37	chr6:56577800-56581400	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:56577800-56581400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr6:56577800-56581600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:56577800-56581600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:56577800-56581600	Enhancers	Brain Anterior Caudate	brain
42	chr6:56577800-56581600	Enhancers	Brain Cingulate Gyrus	brain
43	chr6:56577800-56581600	Enhancers	Brain Hippocampus Middle	brain
44	chr6:56577800-56581600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr6:56577800-56581600	Enhancers	Brain Substantia Nigra	brain
46	chr6:56577800-56581600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr6:56577800-56582600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:56577800-56582800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:56577800-56582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:56577800-56583600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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