Variant report

Variant	rs2270994
Chromosome Location	chr11:48157869-48157870
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	chr11:48147718..48152937-chr11:48156132..48159658,5	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1039484	0.89[YRI][hapmap]
rs10769312	0.86[LWK][hapmap];0.89[YRI][hapmap]
rs10838798	0.89[YRI][hapmap]
rs10838800	0.86[LWK][hapmap];0.89[YRI][hapmap]
rs10838852	0.89[CEU][hapmap]
rs11039516	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039530	0.88[CEU][hapmap]
rs11039537	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039541	0.84[EUR][1000 genomes]
rs11039543	0.88[CEU][hapmap]
rs1483123	0.89[CEU][hapmap]
rs1566732	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17198859	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2270992	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2870080	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2904315	0.95[LWK][hapmap];0.89[YRI][hapmap]
rs4752894	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752899	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752902	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4752904	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6485807	0.95[LWK][hapmap];0.89[YRI][hapmap]
rs7121133	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7395231	0.88[YRI][hapmap]
rs7927965	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv1048554	chr11:48062861-48388686	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv1038210	chr11:48068862-48388686	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
17	nsv1052076	chr11:48077864-48702549	ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
18	nsv869354	chr11:48088580-48783113	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
19	nsv1045734	chr11:48089315-48893207	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
20	nsv467871	chr11:48106486-48694871	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
21	nsv554211	chr11:48106486-48694871	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
22	nsv948502	chr11:48110043-48891877	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
23	nsv1050815	chr11:48126145-48342923	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
24	nsv1043509	chr11:48127618-48616507	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
25	nsv541039	chr11:48127618-48616507	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
26	nsv1049379	chr11:48129034-48374636	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
27	nsv428253	chr11:48133996-48524981	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
28	nsv1051661	chr11:48149295-48616507	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
29	nsv541040	chr11:48149295-48616507	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2270994	ATG13	cis	parietal	SCAN
rs2270994	LOC646813	cis	cerebellum	SCAN
rs2270994	Hs.6637	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48131600-48191600	Weak transcription	Small Intestine	intestine
2	chr11:48137000-48172000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:48137000-48175200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr11:48137200-48161000	Weak transcription	NHDF-Ad	bronchial
5	chr11:48138200-48192600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:48139600-48172200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:48141200-48162800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr11:48141200-48163200	Strong transcription	Fetal Intestine Large	intestine
9	chr11:48143200-48164200	Weak transcription	Ovary	ovary
10	chr11:48144000-48175200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:48145600-48175600	Weak transcription	Fetal Brain Male	brain
12	chr11:48145800-48184200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:48146400-48160200	Weak transcription	Esophagus	oesophagus
14	chr11:48146400-48175400	Weak transcription	Fetal Heart	heart
15	chr11:48146800-48160800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:48147000-48166400	Weak transcription	Fetal Thymus	thymus
17	chr11:48147400-48160800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:48149800-48158600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:48149800-48160200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:48149800-48161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:48149800-48161000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr11:48149800-48161200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:48149800-48174600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:48149800-48190600	Weak transcription	Right Ventricle	heart
25	chr11:48150000-48161000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr11:48150400-48158600	Weak transcription	Left Ventricle	heart
27	chr11:48150400-48161200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:48151200-48164400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr11:48151400-48163000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:48151400-48191600	Weak transcription	Stomach Mucosa	stomach
31	chr11:48151600-48160600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:48151600-48161000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:48151600-48164200	Weak transcription	NHLF	lung
34	chr11:48151600-48174400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:48152000-48158800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:48152000-48159400	Weak transcription	Colonic Mucosa	Colon
37	chr11:48152000-48161000	Weak transcription	Aorta	Aorta
38	chr11:48152000-48165600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:48152000-48175400	Weak transcription	K562	blood
40	chr11:48152200-48158400	Weak transcription	Fetal Brain Female	brain
41	chr11:48152200-48158600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:48152200-48160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:48152200-48160800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:48152200-48161000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:48152200-48161200	Weak transcription	Fetal Muscle Leg	muscle
46	chr11:48152200-48164400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:48152400-48160400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr11:48153400-48158400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:48153400-48158400	Weak transcription	GM12878-XiMat	blood
50	chr11:48153400-48160600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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