Variant report

Variant	rs2701528
Chromosome Location	chr11:63957070-63957071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63929801..63939249-chr11:63945151..63958671,77	MCF-7	breast:
2	chr11:63955085..63958830-chr11:63958900..63961430,4	MCF-7	breast:
3	chr11:63931311..63936745-chr11:63945647..63958123,49	MCF-7	breast:
4	chr11:63950774..63958537-chr11:64070493..64074690,13	MCF-7	breast:
5	chr11:63951197..63955095-chr11:63955593..63958792,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219435	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000173153	Chromatin interaction
ENSG00000133315	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs2246552	0.89[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs2254599	0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs2254709	0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs2325785	1.00[AMR][1000 genomes]
rs2429457	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2508208	0.89[AFR][1000 genomes]
rs2515239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2515240	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2622413	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2622414	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs2622415	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2622416	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2622421	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2622423	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2622431	0.89[ASW][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes]
rs2701525	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2701526	0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2701529	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2701532	1.00[AMR][1000 genomes]
rs2701535	0.89[ASW][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs2701538	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs2845587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2845589	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2845591	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2845595	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs2845598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35525149	1.00[AFR][1000 genomes]
rs4294564	1.00[AFR][1000 genomes]
rs4379854	0.89[ASW][hapmap];0.83[LWK][hapmap];0.86[YRI][hapmap]
rs4587731	1.00[AFR][1000 genomes]
rs4980526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60647009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs611637	0.89[ASW][hapmap];0.96[LWK][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes]
rs620818	0.93[AFR][1000 genomes]
rs633557	0.93[YRI][hapmap];0.95[AFR][1000 genomes]
rs633561	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
6	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
7	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
8	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
9	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
10	nsv897663	chr11:63910153-63962152	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	n/a
11	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
12	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
13	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
14	nsv897665	chr11:63927695-64026144	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
15	nsv897666	chr11:63929493-64026144	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
16	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
17	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
18	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
19	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
20	nsv468595	chr11:63953121-64027888	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
21	nsv555187	chr11:63953121-64027888	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2701528	NUDT22	cis	lymphoblastoid	seeQTL
rs2701528	HBD	trans	lymphoblastoid	seeQTL
rs2701528	NUDT22	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63954600-63957400	Enhancers	Spleen	Spleen
2	chr11:63954600-63960000	Weak transcription	Gastric	stomach
3	chr11:63954600-63967400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:63954800-63958400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:63954800-63960000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:63954800-63960000	Weak transcription	Aorta	Aorta
7	chr11:63955000-63957400	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr11:63955000-63957600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:63955000-63957600	Genic enhancers	Fetal Muscle Leg	muscle
10	chr11:63955000-63958800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr11:63955000-63959400	Weak transcription	Psoas Muscle	Psoas
12	chr11:63955000-63959600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:63955000-63960000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:63955000-63960000	Weak transcription	Esophagus	oesophagus
15	chr11:63955000-63960600	Weak transcription	Fetal Kidney	kidney
16	chr11:63955000-63969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:63955200-63957200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:63955200-63957200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:63955200-63957400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:63955200-63957400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:63955200-63957400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:63955200-63957400	Enhancers	Brain Cingulate Gyrus	brain
23	chr11:63955200-63957400	Genic enhancers	A549	lung
24	chr11:63955200-63959400	Weak transcription	Ovary	ovary
25	chr11:63955200-63959600	Weak transcription	NHEK	skin
26	chr11:63955200-63959800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:63955200-63959800	Weak transcription	Right Ventricle	heart
28	chr11:63955200-63960000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:63955200-63960000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:63955200-63960000	Weak transcription	HSMMtube	muscle
31	chr11:63955200-63960000	Weak transcription	NHDF-Ad	bronchial
32	chr11:63955200-63960400	Weak transcription	HMEC	breast
33	chr11:63955200-63960800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr11:63955200-63971600	Strong transcription	Fetal Intestine Small	intestine
35	chr11:63955200-63974400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:63955200-63975000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:63955200-63975200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:63955400-63957200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr11:63955400-63957200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:63955400-63957200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:63955400-63957600	Genic enhancers	K562	blood
42	chr11:63955400-63959800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:63955400-63959800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:63955400-63960000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:63955400-63960000	Weak transcription	HUVEC	blood vessel
46	chr11:63955400-63960400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr11:63955400-63962000	Weak transcription	Small Intestine	intestine
48	chr11:63955600-63957200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:63955600-63957200	Weak transcription	Colon Smooth Muscle	Colon
50	chr11:63955600-63957400	Genic enhancers	Dnd41	blood

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