Variant report

Variant	rs2296742
Chromosome Location	chr6:33659793-33659794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33657954..33660672-chr6:33660957..33664215,4	MCF-7	breast:
2	chr6:33587314..33592159-chr6:33656861..33661736,6	K562	blood:
3	chr6:33659672..33661992-chr6:33673865..33675730,2	MCF-7	breast:
4	chr6:33546559..33548869-chr6:33658517..33660175,2	K562	blood:

Variant related genes	Relation type
ENSG00000030110	Chromatin interaction
ENSG00000269490	Chromatin interaction
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1014933	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10947430	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10947434	0.92[EUR][1000 genomes]
rs10947435	0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs11759396	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555965	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2147656	0.88[EUR][1000 genomes]
rs2147657	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2229642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274458	0.90[EUR][1000 genomes]
rs2281829	0.87[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296736	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296738	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296739	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2296741	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2966	0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs3227	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818521	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3818523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818524	0.91[EUR][1000 genomes]
rs3818525	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818527	0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818529	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818530	0.87[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4711336	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711337	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711338	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711339	0.83[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4711340	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4711343	0.81[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs4713655	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713658	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713659	0.87[CHD][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4713660	0.88[EUR][1000 genomes]
rs4713661	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713662	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4713665	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713666	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713667	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713669	0.82[EUR][1000 genomes]
rs4713670	0.81[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4713671	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4713672	0.81[JPT][hapmap]
rs4713674	0.81[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs4713675	0.81[JPT][hapmap]
rs542441	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs560111	0.81[JPT][hapmap];0.89[TSI][hapmap]
rs622917	0.81[JPT][hapmap]
rs626156	0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6457739	0.87[CHD][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6904816	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6916949	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6917140	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6919321	0.81[JPT][hapmap]
rs6928010	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6938056	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs749338	0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs749847	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs753890	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs754404	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764752	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764753	0.93[YRI][hapmap]
rs764754	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739505	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7759668	0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7770465	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs791902	0.90[JPT][hapmap]
rs791903	0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs9348924	0.86[JPT][hapmap]
rs9366828	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9368773	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9368776	0.89[EUR][1000 genomes]
rs9380375	0.91[EUR][1000 genomes]
rs9394163	0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs942640	0.92[EUR][1000 genomes]
rs942641	0.81[JPT][hapmap]
rs942643	0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9469566	0.81[CHD][hapmap];0.94[EUR][1000 genomes]
rs9469583	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885771	chr6:33626717-33660143	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2296742	HLA-DMA	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33613200-33660400	Strong transcription	Thymus	Thymus
2	chr6:33615000-33660800	Strong transcription	Fetal Intestine Large	intestine
3	chr6:33619600-33660800	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:33621400-33672600	Strong transcription	Dnd41	blood
6	chr6:33622000-33660000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:33630400-33660800	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr6:33631600-33667000	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr6:33631800-33661200	Weak transcription	Liver	Liver
12	chr6:33636600-33660600	Strong transcription	Colonic Mucosa	Colon
13	chr6:33636800-33660200	Strong transcription	Lung	lung
14	chr6:33636800-33661400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:33637400-33661600	Strong transcription	Esophagus	oesophagus
16	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:33641000-33667800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:33641200-33661600	Strong transcription	NHEK	skin
19	chr6:33641400-33660200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:33641800-33661800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:33642400-33660600	Weak transcription	Brain Germinal Matrix	brain
23	chr6:33643800-33659800	Strong transcription	Adipose Nuclei	Adipose
24	chr6:33644000-33660600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:33644000-33662000	Weak transcription	Fetal Kidney	kidney
26	chr6:33645800-33659800	Strong transcription	Fetal Stomach	stomach
27	chr6:33646000-33660400	Weak transcription	HUVEC	blood vessel
28	chr6:33647200-33659800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr6:33649600-33660600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:33649800-33661400	Strong transcription	Pancreas	Pancrea
31	chr6:33650200-33660400	Strong transcription	Placenta	Placenta
32	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:33651600-33659800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:33651600-33659800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr6:33651600-33660400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:33651600-33660600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:33651800-33659800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:33651800-33659800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:33652000-33660000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:33652000-33661800	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:33653600-33661800	Strong transcription	Hela-S3	cervix
44	chr6:33653800-33660600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:33654000-33660800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:33654600-33660200	Weak transcription	HepG2	liver
47	chr6:33654600-33661600	Weak transcription	Fetal Brain Female	brain
48	chr6:33654800-33659800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:33654800-33661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:33654800-33662600	Weak transcription	Small Intestine	intestine

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