Variant report

Variant	rs3748078
Chromosome Location	chr6:4811597-4811598
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4810817..4812587-chr6:4814121..4815809,2	K562	blood:
2	chr6:4810561..4812233-chr6:4812565..4815063,3	MCF-7	breast:
3	chr6:4800467..4802843-chr6:4809432..4811722,2	MCF-7	breast:
4	chr6:4809930..4812317-chr6:4814309..4817023,2	K562	blood:
5	chr6:4810884..4813153-chr6:4835754..4837513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1016877	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11967994	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11968021	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1265332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1265333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1265334	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1265335	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13199417	0.82[CHB][hapmap]
rs13212871	0.82[CHB][hapmap]
rs17138856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17138859	0.91[CHB][hapmap]
rs17138959	0.83[CHB][hapmap]
rs17138966	0.82[CHB][hapmap]
rs184588	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2179269	0.87[EUR][1000 genomes]
rs2179270	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2326553	0.83[CHB][hapmap]
rs233476	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61610972	0.88[EUR][1000 genomes]
rs62386574	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62386575	0.84[EUR][1000 genomes]
rs62386576	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62386577	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62386578	0.85[EUR][1000 genomes]
rs62386582	0.88[EUR][1000 genomes]
rs62386584	0.88[EUR][1000 genomes]
rs62386585	0.88[EUR][1000 genomes]
rs62386587	0.89[EUR][1000 genomes]
rs62386590	0.87[EUR][1000 genomes]
rs62386591	0.81[EUR][1000 genomes]
rs6910368	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs6918626	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs73362560	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs808593	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs808598	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs808600	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs808606	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs808607	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs808635	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs811251	0.82[CHB][hapmap]
rs9504254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4794800-4818800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:4801800-4811600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr6:4802400-4812000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:4802400-4818800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:4803400-4814600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:4804600-4812000	Weak transcription	Pancreas	Pancrea
7	chr6:4804600-4812200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:4804600-4812200	Weak transcription	HSMMtube	muscle
9	chr6:4806400-4812000	Weak transcription	Esophagus	oesophagus
10	chr6:4806400-4812000	Weak transcription	Gastric	stomach
11	chr6:4806400-4812600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:4806600-4812200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:4806800-4814000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:4806800-4819800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:4806800-4820200	Weak transcription	NHLF	lung
16	chr6:4806800-4820400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:4806800-4829400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:4807000-4812200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:4807000-4817400	Weak transcription	Brain Anterior Caudate	brain
20	chr6:4807000-4821200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:4807200-4819800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:4807200-4827800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:4807400-4812000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:4807400-4812000	Weak transcription	Right Atrium	heart
25	chr6:4807400-4812200	Weak transcription	Fetal Thymus	thymus
26	chr6:4807400-4813400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:4807600-4812400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:4807600-4814600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:4807600-4817000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:4808600-4812600	Enhancers	HepG2	liver
31	chr6:4808800-4818800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:4809200-4813000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:4809400-4814000	Weak transcription	Ovary	ovary
34	chr6:4809600-4811600	Weak transcription	Primary B cells from cord blood	blood
35	chr6:4810200-4812200	Enhancers	HUVEC	blood vessel
36	chr6:4810200-4812800	Enhancers	NH-A	brain
37	chr6:4810200-4812800	Enhancers	NHEK	skin
38	chr6:4810200-4816600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:4810400-4812400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr6:4810400-4812600	Enhancers	Small Intestine	intestine
41	chr6:4810400-4812800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:4810400-4812800	Enhancers	Primary B cells from peripheral blood	blood
43	chr6:4810400-4812800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr6:4810400-4812800	Enhancers	HMEC	breast
45	chr6:4810400-4812800	Enhancers	K562	blood
46	chr6:4810400-4816200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:4810600-4813200	Enhancers	GM12878-XiMat	blood
48	chr6:4810800-4811800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr6:4810800-4812200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:4810800-4812400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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