Variant report

Variant	rs2742488
Chromosome Location	chr11:8977691-8977692
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8976504..8978770-chr11:8984640..8987251,2	K562	blood:
2	chr11:8977155..8979531-chr11:8982227..8985372,3	MCF-7	breast:
3	chr11:8968022..8970706-chr11:8976759..8978871,2	K562	blood:
4	chr11:8977298..8978907-chr11:8986024..8987853,3	K562	blood:
5	chr11:8976172..8977812-chr11:8982786..8984481,2	K562	blood:

Variant related genes	Relation type
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10219366	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1025438	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10734639	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10743094	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10769974	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10769976	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10769977	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840150	0.81[AMR][1000 genomes]
rs10840151	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840153	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840154	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840155	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10840156	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042128	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11042129	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11042131	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12785559	0.87[ASN][1000 genomes]
rs12786377	0.87[ASN][1000 genomes]
rs12790020	0.87[ASN][1000 genomes]
rs12794962	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12798311	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12805109	0.87[ASN][1000 genomes]
rs1347016	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985026	0.87[ASN][1000 genomes]
rs2016844	0.91[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2043218	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2056903	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2116510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163625	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246878	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247038	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2248245	0.81[YRI][hapmap]
rs2252102	0.89[ASN][1000 genomes]
rs2316523	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2316541	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568034	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs2568042	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2568047	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2568069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568074	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568075	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568077	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568079	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568081	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568085	0.93[YRI][hapmap]
rs2568086	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568088	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653556	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2653565	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2653569	0.89[YRI][hapmap]
rs2653587	0.88[AFR][1000 genomes]
rs2653590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653594	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2653597	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2653601	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2653604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653611	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742473	0.87[ASN][1000 genomes]
rs2742486	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742489	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742494	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2742495	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742496	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742497	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742504	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742505	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2742512	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742513	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742521	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs3751063	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3751065	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3751066	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3751068	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3763911	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3763912	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4370967	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4909951	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4910313	0.87[ASN][1000 genomes]
rs7106152	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7124403	0.87[ASN][1000 genomes]
rs72851596	0.88[ASN][1000 genomes]
rs72852790	0.98[ASN][1000 genomes]
rs72853712	0.98[ASN][1000 genomes]
rs7932377	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7940895	0.91[ASN][1000 genomes]
rs7942026	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7951226	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs909464	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9300096	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs982273	0.88[CEU][hapmap];0.88[JPT][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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2742488	C11orf17	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:8954400-8984400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:8957000-8980800	Weak transcription	Fetal Heart	heart
4	chr11:8963200-8985000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:8965800-8984800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:8966400-8984000	Weak transcription	Fetal Brain Male	brain
7	chr11:8966800-8980800	Weak transcription	Small Intestine	intestine
8	chr11:8968000-8978200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:8968000-8978400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:8968200-8980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:8968200-8985000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:8968400-8978600	Strong transcription	Liver	Liver
13	chr11:8968400-8979000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:8968400-8979200	Strong transcription	Primary B cells from cord blood	blood
15	chr11:8968600-8977800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr11:8968600-8978000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:8968600-8978000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:8968600-8978800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr11:8968600-8978800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr11:8968600-8979400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr11:8968600-8981000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr11:8968800-8978000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr11:8968800-8978000	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr11:8968800-8978000	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:8968800-8978400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:8968800-8978400	Strong transcription	Fetal Intestine Large	intestine
27	chr11:8968800-8978600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:8968800-8978600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:8968800-8978600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr11:8968800-8978600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:8968800-8978800	Strong transcription	Fetal Muscle Leg	muscle
32	chr11:8968800-8978800	Strong transcription	Placenta	Placenta
33	chr11:8968800-8978800	Strong transcription	Left Ventricle	heart
34	chr11:8968800-8979200	Strong transcription	Adipose Nuclei	Adipose
35	chr11:8968800-8980800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr11:8969000-8977800	Strong transcription	Fetal Thymus	thymus
37	chr11:8969000-8978000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:8969000-8978000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:8969000-8978600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:8969000-8979200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr11:8969400-8978600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:8969400-8980800	Weak transcription	HSMMtube	muscle
43	chr11:8970200-8981000	Weak transcription	NHEK	skin
44	chr11:8970400-8978400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:8970600-8984400	Weak transcription	Right Ventricle	heart
46	chr11:8970600-8985000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr11:8970800-8980800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:8970800-8984400	Weak transcription	A549	lung
49	chr11:8971000-8978800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr11:8971000-8980600	Weak transcription	Psoas Muscle	Psoas

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