Variant report

Variant	rs12804000
Chromosome Location	chr11:17187178-17187179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:17186616..17189507-chr11:17190943..17193289,3	K562	blood:
2	chr11:17154024..17158946-chr11:17185264..17188139,4	K562	blood:
3	chr11:17183106..17184886-chr11:17186963..17189434,2	MCF-7	breast:
4	chr11:17182736..17185668-chr11:17187012..17188861,2	K562	blood:
5	chr11:17182055..17184280-chr11:17186207..17188512,3	K562	blood:
6	chr11:17186572..17188105-chr11:17229637..17231932,2	K562	blood:

Variant related genes	Relation type
ENSG00000011405	Chromatin interaction
ENSG00000070081	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10741724	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10766381	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10832733	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832734	0.82[AMR][1000 genomes]
rs10832735	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10832736	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10832739	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832743	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10832745	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832746	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832747	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10832748	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11024143	0.85[EUR][1000 genomes]
rs11024148	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11024158	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024159	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024163	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024204	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11024207	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11024208	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11024227	0.82[EUR][1000 genomes]
rs1125737	0.90[EUR][1000 genomes]
rs11821773	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12280930	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286505	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1236309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1236310	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1685932	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1979603	0.89[EUR][1000 genomes]
rs1989405	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008905	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2052188	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs214900	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs214901	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs214904	0.86[ASN][1000 genomes]
rs214906	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs214907	0.80[ASN][1000 genomes]
rs214909	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214910	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214911	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs214912	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs214913	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs214914	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214915	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214916	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214917	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs214918	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214919	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214920	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214921	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214922	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214923	0.80[ASN][1000 genomes]
rs214925	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs214926	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs214927	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs214933	0.88[ASN][1000 genomes]
rs214935	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs214936	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs214937	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs214939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs214940	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2171615	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35933265	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4356203	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4509731	0.87[EUR][1000 genomes]
rs511119	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512852	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527810	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536628	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542274	0.92[ASN][1000 genomes]
rs545773	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550667	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553711	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567033	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs577207	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs589319	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59192183	0.84[EUR][1000 genomes]
rs594034	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598946	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603618	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61357262	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs615358	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs618331	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61881888	0.80[EUR][1000 genomes]
rs620241	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621246	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635802	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486354	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs651513	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656623	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662711	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664382	0.86[ASN][1000 genomes]
rs667984	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677042	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs677540	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680205	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101686	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7106705	0.86[EUR][1000 genomes]
rs7107283	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7118006	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118443	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7123301	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125607	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7342262	0.89[EUR][1000 genomes]
rs7396382	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7396958	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7478986	0.93[EUR][1000 genomes]
rs7925692	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7932916	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7935219	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7937176	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7940418	0.88[EUR][1000 genomes]
rs7946010	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7949699	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

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	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	nsv7691	chr11:17151593-17196894	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12804000	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs12804000	OR7E14P	cis	Esophagus Mucosa	GTEx
rs12804000	OR7E14P	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17130200-17203800	Weak transcription	Aorta	Aorta
2	chr11:17144200-17192800	Weak transcription	NHDF-Ad	bronchial
3	chr11:17156600-17219200	Weak transcription	HSMMtube	muscle
4	chr11:17158000-17215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:17165200-17215200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:17166200-17190200	Weak transcription	NH-A	brain
7	chr11:17167000-17188600	Weak transcription	Fetal Stomach	stomach
8	chr11:17167000-17188800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:17167400-17190200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:17167400-17190400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:17167400-17204400	Weak transcription	Thymus	Thymus
12	chr11:17167400-17212600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr11:17167400-17228000	Weak transcription	Fetal Thymus	thymus
14	chr11:17168000-17190200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:17168200-17193800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr11:17169400-17190600	Weak transcription	HSMM	muscle
17	chr11:17172600-17214600	Weak transcription	Fetal Brain Female	brain
18	chr11:17173600-17190200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:17176600-17190200	Weak transcription	Fetal Intestine Large	intestine
20	chr11:17176800-17188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:17176800-17190200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:17177000-17187800	Enhancers	HUVEC	blood vessel
23	chr11:17177000-17189200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:17178200-17188200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:17178400-17188600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:17178600-17189800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:17178800-17195000	Weak transcription	Brain Substantia Nigra	brain
28	chr11:17179600-17190000	Weak transcription	Fetal Kidney	kidney
29	chr11:17181200-17187200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr11:17181400-17187200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:17181400-17194400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:17182000-17196800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:17182200-17196400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:17182200-17196800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:17182400-17190200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:17182600-17188400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:17183200-17187400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr11:17183400-17187400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr11:17183400-17187600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:17183600-17187400	Enhancers	Left Ventricle	heart
41	chr11:17184200-17191800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:17184400-17189200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:17184400-17189800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:17184400-17190000	Weak transcription	Dnd41	blood
45	chr11:17184400-17190200	Weak transcription	Primary T cells from cord blood	blood
46	chr11:17184400-17190200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:17184400-17190400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:17184400-17193400	Weak transcription	Colon Smooth Muscle	Colon
49	chr11:17184600-17188600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr11:17184800-17187200	Enhancers	Primary neutrophils fromperipheralblood	blood

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