Variant report

Variant	rs542274
Chromosome Location	chr11:17207433-17207434
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	chr11:17206803..17209141-chr11:17217436..17220407,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10741724	0.81[AFR][1000 genomes]
rs10766381	0.86[AFR][1000 genomes]
rs10832733	0.82[CHB][hapmap];0.92[YRI][hapmap]
rs10832739	0.90[ASN][1000 genomes]
rs10832743	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10832746	0.84[AFR][1000 genomes]
rs10832747	0.87[YRI][hapmap]
rs10832748	0.81[AFR][1000 genomes]
rs10832752	0.96[CEU][hapmap];0.84[CHB][hapmap]
rs11024148	0.92[YRI][hapmap]
rs11024158	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs11024159	0.86[ASN][1000 genomes]
rs11024163	0.88[ASN][1000 genomes]
rs11024204	0.92[YRI][hapmap]
rs11024223	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs12280930	0.92[CHB][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs12286505	0.92[CHB][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs1236309	0.87[ASN][1000 genomes]
rs1236310	0.81[ASN][1000 genomes]
rs12804000	0.92[ASN][1000 genomes]
rs1685932	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1989405	0.92[ASN][1000 genomes]
rs2052188	0.84[ASN][1000 genomes]
rs214071	0.84[CHB][hapmap]
rs214075	0.82[CHB][hapmap]
rs214101	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs214900	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs214901	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs214902	0.85[EUR][1000 genomes]
rs214904	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214906	0.91[ASN][1000 genomes]
rs214907	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs214910	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs214913	0.81[AFR][1000 genomes]
rs214914	0.91[YRI][hapmap]
rs214915	0.81[AFR][1000 genomes]
rs214916	0.91[AFR][1000 genomes]
rs214918	0.81[AFR][1000 genomes]
rs214919	0.91[AFR][1000 genomes]
rs214920	0.81[AFR][1000 genomes]
rs214921	0.81[AFR][1000 genomes]
rs214922	0.81[AFR][1000 genomes]
rs214923	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs214925	0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs214927	0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs214933	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs214935	0.92[CHB][hapmap];0.92[YRI][hapmap];0.89[ASN][1000 genomes]
rs214936	0.91[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs214937	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs214939	0.92[CHB][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs214940	0.91[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2171615	0.88[AFR][1000 genomes]
rs511119	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs512852	0.92[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs527810	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs536628	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs545773	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs550667	0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs553711	0.92[ASN][1000 genomes]
rs567033	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577207	0.84[AFR][1000 genomes]
rs589319	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs594034	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs598946	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs603618	0.83[YRI][hapmap]
rs61357262	0.81[AFR][1000 genomes]
rs615358	0.92[CHB][hapmap];0.90[ASN][1000 genomes]
rs618331	0.92[YRI][hapmap]
rs620241	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs621246	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs635802	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6486352	0.90[ASN][1000 genomes]
rs6486354	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs651513	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs656623	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs662711	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs664382	0.91[ASN][1000 genomes]
rs667984	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs677042	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677540	0.91[CHB][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs680205	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7118006	0.85[ASN][1000 genomes]
rs7123301	0.91[CHB][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs7125607	0.92[YRI][hapmap]
rs7342262	0.81[YRI][hapmap]
rs7396382	0.88[ASN][1000 genomes]
rs7396958	0.91[ASN][1000 genomes]
rs7925692	0.87[YRI][hapmap]
rs7929927	0.82[CHB][hapmap]
rs7935219	0.88[ASN][1000 genomes]
rs7937176	0.88[YRI][hapmap]
rs7938820	0.87[YRI][hapmap]
rs7946010	0.91[ASN][1000 genomes]
rs7949699	0.83[CHB][hapmap]

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	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv469762	chr11:17170690-17320691	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv482905	chr11:17170690-17320691	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv553569	chr11:17201219-17211182	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv553570	chr11:17203765-17210885	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs542274	NUCB2	cis	multi-tissue	Pritchard
rs542274	OR7E14P	cis	Esophagus Mucosa	GTEx
rs542274	OR7E14P	cis	Nerve Tibial	GTEx
rs542274	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs542274	NUCB2	cis	Lymphoblastoid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17156600-17219200	Weak transcription	HSMMtube	muscle
2	chr11:17158000-17215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:17165200-17215200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:17167400-17212600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:17167400-17228000	Weak transcription	Fetal Thymus	thymus
6	chr11:17172600-17214600	Weak transcription	Fetal Brain Female	brain
7	chr11:17184800-17228800	Weak transcription	Esophagus	oesophagus
8	chr11:17185800-17212800	Weak transcription	Pancreas	Pancrea
9	chr11:17187000-17212600	Weak transcription	Brain Hippocampus Middle	brain
10	chr11:17187000-17228000	Weak transcription	Colonic Mucosa	Colon
11	chr11:17187200-17210000	Weak transcription	Psoas Muscle	Psoas
12	chr11:17187200-17210000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr11:17187200-17212600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:17187200-17214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:17187200-17214200	Weak transcription	Right Ventricle	heart
16	chr11:17187200-17226800	Weak transcription	Small Intestine	intestine
17	chr11:17191000-17207600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:17191000-17210000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr11:17191000-17210200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:17191000-17220600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:17191200-17208600	Weak transcription	GM12878-XiMat	blood
22	chr11:17191200-17209800	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:17191200-17210000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:17191200-17210000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr11:17191200-17212200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr11:17191200-17212400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr11:17191200-17212600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:17191200-17213000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr11:17191200-17213000	Weak transcription	Dnd41	blood
30	chr11:17191200-17227800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:17191400-17212800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr11:17191400-17213000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:17191400-17214400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:17191600-17212200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:17191800-17212400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr11:17191800-17212800	Weak transcription	Fetal Kidney	kidney
37	chr11:17192000-17214400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr11:17192400-17214400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:17192400-17217800	Weak transcription	Stomach Mucosa	stomach
40	chr11:17193200-17212400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:17193800-17213000	Weak transcription	NH-A	brain
42	chr11:17194000-17209800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:17194000-17210200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:17194000-17212400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:17194000-17212400	Weak transcription	Hela-S3	cervix
46	chr11:17194000-17212600	Weak transcription	Placenta	Placenta
47	chr11:17194000-17212800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:17194000-17212800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:17194000-17212800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:17194000-17212800	Weak transcription	Ovary	ovary

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