Variant report

Variant	rs2296748
Chromosome Location	chr6:33745071-33745072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:33744237-33745292	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:33744811-33745167	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:33745069-33745541	K562	blood:	n/a	n/a
4	POLR2A	chr6:33745033-33745818	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:33744376-33745278	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:33743524-33745765	K562	blood:	n/a	n/a
7	POLR2A	chr6:33745027-33745316	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:33745071-33745088	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:33744919-33745329	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:33744248-33745335	A549	lung:	n/a	n/a
11	POLR2A	chr6:33743729-33745633	K562	blood:	n/a	n/a
12	ZKSCAN1	chr6:33745029-33745106	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33743352..33745913-chr6:33755354..33756938,3	MCF-7	breast:
2	chr6:33743776..33747465-chr6:33751783..33755243,5	MCF-7	breast:

Variant related genes	Relation type
LEMD2	TF binding region
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11752297	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12190029	0.84[AFR][1000 genomes]
rs1359781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2013365	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2013381	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2281816	0.86[ASW][hapmap]
rs2296743	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2296746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296747	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395402	0.96[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2395449	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3763260	0.86[ASW][hapmap]
rs3793079	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806108	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806109	0.93[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3806110	0.93[ASW][hapmap];0.84[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4342423	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711349	0.91[AFR][1000 genomes]
rs4711351	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711355	0.81[AFR][1000 genomes]
rs4713679	0.83[AFR][1000 genomes]
rs4713681	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713682	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713683	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713684	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6457741	0.81[AFR][1000 genomes]
rs6904716	0.94[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap]
rs6904991	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6920075	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6922275	0.81[AFR][1000 genomes]
rs6925273	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6929696	0.82[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs747695	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs751726	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs751728	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755496	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs755497	0.81[CHB][hapmap]
rs756137	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9357164	0.81[AFR][1000 genomes]
rs9366829	0.83[CHD][hapmap];0.88[JPT][hapmap]
rs9380376	0.94[JPT][hapmap]
rs9380378	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394165	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9394166	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];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9394167	0.89[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9394168	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs943467	0.88[CHB][hapmap]
rs943471	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs943474	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs943475	0.89[LWK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs943477	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs943478	0.81[AFR][1000 genomes]
rs943479	0.96[YRI][hapmap];0.81[AFR][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	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
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2296748	PPARD	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33738600-33753200	Strong transcription	Thymus	Thymus
2	chr6:33739000-33746000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:33739600-33752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:33739600-33754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:33739800-33752400	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:33739800-33752600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:33739800-33753000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr6:33739800-33753000	Strong transcription	Primary T cells from cord blood	blood
9	chr6:33739800-33753000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr6:33739800-33753600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:33740000-33746000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:33740000-33749000	Strong transcription	Brain Anterior Caudate	brain
13	chr6:33740000-33752400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:33740000-33752600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:33740000-33752600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:33740000-33752800	Strong transcription	Dnd41	blood
17	chr6:33740000-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:33740000-33753000	Strong transcription	HepG2	liver
19	chr6:33740000-33753200	Strong transcription	Primary hematopoietic stem cells	blood
20	chr6:33740000-33753600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr6:33740000-33753600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:33740200-33745800	Strong transcription	Brain Germinal Matrix	brain
23	chr6:33740200-33746600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:33740200-33747800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:33740200-33748400	Weak transcription	Fetal Heart	heart
26	chr6:33740200-33748600	Weak transcription	Right Atrium	heart
27	chr6:33740200-33748800	Strong transcription	Osteobl	bone
28	chr6:33740200-33749200	Strong transcription	Gastric	stomach
29	chr6:33740200-33749400	Strong transcription	Lung	lung
30	chr6:33740200-33750000	Strong transcription	Pancreas	Pancrea
31	chr6:33740200-33751600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:33740200-33751800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:33740200-33752400	Strong transcription	Rectal Smooth Muscle	rectum
34	chr6:33740200-33752600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:33740200-33753000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:33740200-33753400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr6:33740200-33754000	Strong transcription	Primary B cells from cord blood	blood
38	chr6:33740400-33745800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:33740400-33747200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:33740400-33747800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:33740400-33747800	Strong transcription	Left Ventricle	heart
42	chr6:33740400-33749000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:33740400-33749200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:33740400-33752600	Strong transcription	Colon Smooth Muscle	Colon
45	chr6:33740400-33752800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:33740400-33753200	Strong transcription	Aorta	Aorta
47	chr6:33740400-33753600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:33740600-33746000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:33740600-33747400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:33740600-33747600	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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