Variant report

Variant	rs4143828
Chromosome Location	chr6:56412554-56412555
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	EP300	chr6:56412489-56412803	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr6:56412284-56412621	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56406850..56409641-chr6:56410586..56415474,8	K562	blood:
2	chr6:56403956..56410167-chr6:56410483..56413824,9	K562	blood:

Variant related genes	Relation type
DST	TF binding region
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs11751569	0.82[YRI][hapmap]
rs11753813	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs11756977	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11757910	0.80[YRI][hapmap]
rs11757941	0.82[YRI][hapmap]
rs11758339	0.90[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap]
rs11759493	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11961668	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12174955	0.86[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12527139	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13194746	0.82[EUR][1000 genomes]
rs13204556	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13218268	0.82[YRI][hapmap]
rs13219448	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359068	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1359070	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1535612	0.87[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap]
rs16887974	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064591	0.82[EUR][1000 genomes]
rs2273972	0.86[CEU][hapmap]
rs2273973	0.87[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap]
rs2273974	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2294697	0.82[YRI][hapmap]
rs2397221	0.82[YRI][hapmap]
rs2397226	0.87[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2894837	0.81[CHB][hapmap]
rs34954984	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35671304	0.81[EUR][1000 genomes]
rs35926142	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4130060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4143827	0.82[EUR][1000 genomes]
rs4236139	0.86[CEU][hapmap]
rs4236140	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4236141	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4236142	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236143	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4236144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236145	1.00[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]
rs4283892	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4329120	0.82[EUR][1000 genomes]
rs4331988	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4346846	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4454141	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4466244	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4473850	0.84[EUR][1000 genomes]
rs4499917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4544910	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs45486696	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4712132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715625	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4715626	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4715627	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4715628	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs4715629	0.87[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs4715630	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];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715631	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs595238	0.91[YRI][hapmap]
rs636389	0.91[YRI][hapmap]
rs6459161	0.86[CEU][hapmap]
rs6459163	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6904202	0.86[CEU][hapmap]
rs6906792	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6907917	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6911502	0.91[YRI][hapmap]
rs6913572	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6914184	0.85[EUR][1000 genomes]
rs6922770	0.87[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs6927258	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs6939305	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72877350	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7741295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7743011	0.82[EUR][1000 genomes]
rs7746753	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7755361	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7755573	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7758054	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7759875	0.90[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs7760640	0.87[CEU][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs7760695	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7761281	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7762629	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7775847	0.82[YRI][hapmap]
rs9296848	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9296849	0.82[EUR][1000 genomes]
rs9296850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349823	0.84[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9349825	0.82[AMR][1000 genomes]
rs9349826	0.82[EUR][1000 genomes]
rs9349828	0.93[JPT][hapmap]
rs9357921	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357922	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370533	0.86[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs9370534	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap]
rs9370535	0.95[CEU][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9396213	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs9396214	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9396215	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9396220	0.80[EUR][1000 genomes]
rs9464389	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9475713	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs9475714	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs9475716	0.90[EUR][1000 genomes];0.91[ASN][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56412800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:56408200-56413000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:56408200-56413400	Weak transcription	NHLF	lung
4	chr6:56408200-56414600	Weak transcription	Aorta	Aorta
5	chr6:56408200-56415200	Weak transcription	Right Atrium	heart
6	chr6:56408200-56415400	Weak transcription	Ovary	ovary
7	chr6:56408200-56416200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:56408200-56416600	Weak transcription	Left Ventricle	heart
9	chr6:56408200-56416800	Weak transcription	Brain Germinal Matrix	brain
10	chr6:56408200-56416800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:56408200-56417000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:56408200-56417000	Weak transcription	Fetal Brain Female	brain
13	chr6:56408200-56417200	Weak transcription	Fetal Brain Male	brain
14	chr6:56408200-56417400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:56408200-56419400	Weak transcription	Placenta	Placenta
16	chr6:56408200-56419800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:56408200-56440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:56408200-56440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:56408400-56412800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:56408400-56413000	Weak transcription	Fetal Intestine Large	intestine
22	chr6:56408400-56413200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:56408400-56413800	Weak transcription	HUVEC	blood vessel
24	chr6:56408400-56414200	Weak transcription	GM12878-XiMat	blood
25	chr6:56408400-56414800	Weak transcription	Adipose Nuclei	Adipose
26	chr6:56408400-56415600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:56408400-56416200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:56408400-56416200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:56408400-56416200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:56408400-56416400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:56408400-56416600	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:56408400-56416800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:56408400-56416800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:56408400-56416800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:56408400-56416800	Weak transcription	Fetal Stomach	stomach
36	chr6:56408400-56417400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:56408400-56417400	Weak transcription	HMEC	breast
38	chr6:56408400-56430800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr6:56408600-56415200	Weak transcription	HSMMtube	muscle
40	chr6:56408600-56417200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:56408600-56417400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:56409000-56413000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr6:56409000-56413400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:56409000-56413600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:56409000-56414400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:56409000-56415200	Weak transcription	NHEK	skin
47	chr6:56409000-56416000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:56409000-56416200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:56409000-56416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:56409200-56413200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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