Variant report

Variant	rs2029378
Chromosome Location	chr11:46454798-46454799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46448640..46451542-chr11:46454493..46456535,2	K562	blood:
2	chr11:46450955..46452945-chr11:46454344..46456750,3	MCF-7	breast:
3	chr11:46448640..46452068-chr11:46454493..46457739,3	K562	blood:

Variant related genes	Relation type
ENSG00000244313	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10734546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11038924	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12099188	0.80[AFR][1000 genomes]
rs1466634	1.00[YRI][hapmap]
rs1489189	1.00[YRI][hapmap]
rs1489190	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1489193	1.00[YRI][hapmap]
rs1812657	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1873129	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2046766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2046767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2087360	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2087361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2864071	1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2864836	1.00[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs34217002	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34444424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35267642	1.00[AMR][1000 genomes]
rs35715394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35935319	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4367921	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs4376875	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4433539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4508179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4550197	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56991558	1.00[AMR][1000 genomes]
rs57923752	0.80[AFR][1000 genomes]
rs58314136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58770070	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60026983	0.80[AFR][1000 genomes]
rs60147143	0.80[AFR][1000 genomes]
rs60162610	1.00[AMR][1000 genomes]
rs61451984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61514976	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61693609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6485681	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73449906	0.80[AFR][1000 genomes]
rs73449908	0.80[AFR][1000 genomes]
rs73449917	0.80[AFR][1000 genomes]
rs73449920	0.80[AFR][1000 genomes]
rs73449937	0.80[AFR][1000 genomes]
rs73449939	0.80[AFR][1000 genomes]
rs73449943	0.80[AFR][1000 genomes]
rs73449951	0.80[AFR][1000 genomes]
rs73449956	0.80[AFR][1000 genomes]
rs73449974	0.80[AFR][1000 genomes]
rs73449985	0.80[AFR][1000 genomes]
rs73450002	0.80[AFR][1000 genomes]
rs73451811	0.80[AFR][1000 genomes]
rs73451819	0.80[AFR][1000 genomes]
rs73451822	0.80[AFR][1000 genomes]
rs73451825	0.80[AFR][1000 genomes]
rs73451848	0.80[AFR][1000 genomes]
rs73451858	0.80[AFR][1000 genomes]
rs73451860	0.80[AFR][1000 genomes]
rs73451863	0.80[AFR][1000 genomes]
rs73451880	0.80[AFR][1000 genomes]
rs73451885	0.80[AFR][1000 genomes]
rs73451898	0.80[AFR][1000 genomes]
rs73464080	1.00[AMR][1000 genomes]
rs73466031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73466069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73466088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73466094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73466095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73466099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467917	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467919	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467920	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467936	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467938	1.00[AMR][1000 genomes]
rs73467941	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467944	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467947	0.80[AFR][1000 genomes]
rs73467950	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467963	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73467964	0.80[AFR][1000 genomes]
rs73467966	0.80[AFR][1000 genomes]
rs7924437	0.91[AFR][1000 genomes]
rs7924695	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7928869	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7942788	1.00[YRI][hapmap]
rs901995	1.00[ASW][hapmap]
rs901999	1.00[ASW][hapmap]
rs967754	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv554202	chr11:46334239-46469900	Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1050614	chr11:46414720-46496732	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541029	chr11:46442658-46460232	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46417800-46463400	Weak transcription	Fetal Brain Male	brain
2	chr11:46426800-46468800	Weak transcription	Psoas Muscle	Psoas
3	chr11:46430200-46456000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:46430600-46455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:46433600-46466400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr11:46436600-46466400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:46437400-46455000	Weak transcription	Stomach Mucosa	stomach
8	chr11:46438000-46461400	Strong transcription	Primary T cells from cord blood	blood
9	chr11:46438400-46457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:46438400-46459600	Strong transcription	Dnd41	blood
11	chr11:46440400-46466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:46443200-46454800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:46443800-46454800	Weak transcription	NHLF	lung
14	chr11:46444000-46456600	Weak transcription	Fetal Heart	heart
15	chr11:46444800-46457200	Weak transcription	Small Intestine	intestine
16	chr11:46445800-46456600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr11:46445800-46458000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:46447000-46457400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:46447200-46457600	Strong transcription	Fetal Stomach	stomach
20	chr11:46447600-46457600	Strong transcription	Liver	Liver
21	chr11:46447600-46457600	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:46447800-46456200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:46447800-46460600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:46448200-46457800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr11:46448600-46457600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:46448800-46457600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:46448800-46457600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr11:46449000-46456600	Strong transcription	Fetal Muscle Leg	muscle
29	chr11:46449000-46457400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:46449600-46457800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr11:46450000-46457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:46450400-46458000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:46450600-46456800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:46450800-46456600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:46450800-46456800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:46450800-46457600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:46451000-46454800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:46451000-46456600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr11:46451000-46456800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr11:46451000-46457000	Strong transcription	Fetal Intestine Large	intestine
41	chr11:46451000-46457400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:46451000-46457400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr11:46451000-46457400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr11:46451000-46457400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:46451000-46457600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr11:46451000-46457800	Strong transcription	HepG2	liver
47	chr11:46451000-46458000	Strong transcription	Placenta	Placenta
48	chr11:46451000-46459600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr11:46451200-46454800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:46451200-46457800	Strong transcription	Fetal Thymus	thymus

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