Variant report

Variant	rs10946837
Chromosome Location	chr6:26540844-26540845
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26537837..26539714-chr6:26539743..26541511,2	MCF-7	breast:
2	chr6:26284431..26286748-chr6:26538592..26541230,2	K562	blood:
3	chr6:26188869..26191553-chr6:26538652..26541093,2	K562	blood:
4	chr6:26535400..26541597-chr6:26593643..26598951,8	K562	blood:
5	chr6:26216321..26218789-chr6:26539322..26541889,2	K562	blood:

Variant related genes	Relation type
ENSG00000187990	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000146109	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1001687	0.91[EUR][1000 genomes]
rs10214634	0.96[EUR][1000 genomes]
rs10223789	0.86[EUR][1000 genomes]
rs10223792	0.86[EUR][1000 genomes]
rs10484442	0.96[EUR][1000 genomes]
rs1056347	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1056667	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1056668	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1078679	0.94[EUR][1000 genomes]
rs10946834	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10946835	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11752946	0.93[EUR][1000 genomes]
rs11754138	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11756120	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12526680	0.92[EUR][1000 genomes]
rs12663883	0.90[EUR][1000 genomes]
rs12663894	0.89[EUR][1000 genomes]
rs12665431	0.89[EUR][1000 genomes]
rs1321479	0.87[EUR][1000 genomes]
rs1321480	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1321481	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1321482	0.90[EUR][1000 genomes]
rs1535276	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1535277	0.84[EUR][1000 genomes]
rs1570059	0.91[EUR][1000 genomes]
rs1570060	0.91[EUR][1000 genomes]
rs1570061	0.90[EUR][1000 genomes]
rs1884946	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1884947	0.94[EUR][1000 genomes]
rs1884948	0.94[EUR][1000 genomes]
rs1884949	0.94[EUR][1000 genomes]
rs1977201	0.91[EUR][1000 genomes]
rs2208331	0.88[EUR][1000 genomes]
rs2224380	0.96[EUR][1000 genomes]
rs2255070	0.87[EUR][1000 genomes]
rs2393669	0.83[EUR][1000 genomes]
rs2393670	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28558133	0.86[EUR][1000 genomes]
rs35355150	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3736781	0.87[EUR][1000 genomes]
rs3736782	0.87[EUR][1000 genomes]
rs3757151	0.85[EUR][1000 genomes]
rs4573	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713006	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4713008	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4871	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55930917	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6456733	0.95[EUR][1000 genomes]
rs6456734	0.93[EUR][1000 genomes]
rs6456735	0.91[EUR][1000 genomes]
rs6903973	0.87[EUR][1000 genomes]
rs6909277	0.88[EUR][1000 genomes]
rs6910899	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6910930	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6913398	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913462	0.90[EUR][1000 genomes]
rs6913877	0.90[EUR][1000 genomes]
rs6918360	0.90[EUR][1000 genomes]
rs6918506	0.90[EUR][1000 genomes]
rs6918854	0.90[EUR][1000 genomes]
rs6922824	0.96[EUR][1000 genomes]
rs6924838	0.94[EUR][1000 genomes]
rs6924865	0.89[EUR][1000 genomes]
rs6925703	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6925783	0.91[EUR][1000 genomes]
rs6925895	0.94[EUR][1000 genomes]
rs6926629	0.87[EUR][1000 genomes]
rs6930120	0.95[EUR][1000 genomes]
rs6932156	0.94[EUR][1000 genomes]
rs6932350	0.91[EUR][1000 genomes]
rs6932865	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6933176	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6940053	0.95[EUR][1000 genomes]
rs6940188	0.95[EUR][1000 genomes]
rs6941022	0.96[EUR][1000 genomes]
rs767471	0.95[EUR][1000 genomes]
rs7753565	0.81[EUR][1000 genomes]
rs9295694	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9295695	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9295698	0.95[EUR][1000 genomes]
rs9357010	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9358952	0.82[EUR][1000 genomes]
rs9358954	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9379887	0.88[EUR][1000 genomes]
rs9393729	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9393731	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9393732	0.90[EUR][1000 genomes]
rs9461259	0.87[EUR][1000 genomes]
rs9461267	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9461270	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461271	0.96[EUR][1000 genomes]
rs9461272	0.86[EUR][1000 genomes]
rs9467773	0.84[EUR][1000 genomes]
rs9467774	0.87[EUR][1000 genomes]
rs9467775	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9467776	0.89[EUR][1000 genomes]
rs9467778	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9467779	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9467782	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467783	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467784	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9467787	0.95[EUR][1000 genomes]
rs9467791	0.95[EUR][1000 genomes]
rs9467796	0.94[EUR][1000 genomes]
rs9467797	0.94[EUR][1000 genomes]
rs9467798	0.90[EUR][1000 genomes]
rs9467799	0.87[EUR][1000 genomes]
rs9467800	0.87[EUR][1000 genomes]
rs9467802	0.86[EUR][1000 genomes]
rs9986382	0.96[EUR][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription 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 miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10946837	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs10946837	HMGN4	cis	Whole Blood	GTEx
rs10946837	HMGN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26539200-26545400	Weak transcription	Gastric	stomach
2	chr6:26539200-26550600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:26539400-26542800	Weak transcription	Liver	Liver
4	chr6:26539400-26546000	Weak transcription	Ovary	ovary
5	chr6:26539400-26550600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:26539600-26541200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr6:26539600-26541400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:26539600-26541800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:26539600-26542000	Weak transcription	NH-A	brain
10	chr6:26539600-26542200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr6:26539600-26542400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:26539600-26542600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:26539600-26542800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:26539600-26543000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:26539600-26543200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:26539600-26544600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:26539600-26544800	Weak transcription	Psoas Muscle	Psoas
18	chr6:26539600-26544800	Weak transcription	HSMMtube	muscle
19	chr6:26539600-26545200	Weak transcription	Spleen	Spleen
20	chr6:26539600-26545400	Weak transcription	HUVEC	blood vessel
21	chr6:26539600-26549800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:26539600-26550400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:26539600-26550400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:26539600-26550400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:26539600-26550600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:26539600-26553000	Weak transcription	Fetal Heart	heart
27	chr6:26539800-26541800	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr6:26539800-26542400	Weak transcription	Placenta	Placenta
29	chr6:26539800-26543000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:26539800-26544800	Weak transcription	Left Ventricle	heart
31	chr6:26539800-26544800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:26539800-26545200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:26539800-26545200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:26539800-26550400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:26539800-26550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:26539800-26550800	Weak transcription	Pancreas	Pancrea
37	chr6:26540000-26541200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
38	chr6:26540000-26544800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:26540000-26545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:26540000-26545400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:26540000-26545400	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:26540000-26550800	Weak transcription	Lung	lung
43	chr6:26540200-26541200	Strong transcription	Fetal Thymus	thymus
44	chr6:26540200-26541200	Genic enhancers	A549	lung
45	chr6:26540200-26541200	Genic enhancers	NHDF-Ad	bronchial
46	chr6:26540200-26541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:26540200-26541600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:26540200-26541600	Weak transcription	NHLF	lung
49	chr6:26540200-26541800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:26540200-26542000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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