Variant report

Variant	rs541178
Chromosome Location	chr6:74205631-74205632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr6:74205399-74205638	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:74205310..74209199-chr6:74229303..74231458,3	K562	blood:
2	chr6:74205280..74208067-chr6:74222122..74224790,3	K562	blood:
3	chr6:74173316..74175566-chr6:74205182..74206787,2	K562	blood:
4	chr6:74205300..74207492-chr6:74221549..74225584,4	K562	blood:
5	chr6:74200715..74203262-chr6:74205421..74207226,2	K562	blood:
6	chr6:74203362..74206596-chr6:74207328..74210282,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000223821	TF binding region
ENSG00000156508	Chromatin interaction
ENSG00000223821	Chromatin interaction
ENSG00000207023	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs12198468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1245345	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1245346	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1245348	0.90[EUR][1000 genomes]
rs1390080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1691341	0.82[GIH][hapmap]
rs1703461	1.00[CEU][hapmap]
rs1713862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1741886	1.00[CEU][hapmap]
rs1741895	0.82[GIH][hapmap]
rs2643196	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28576277	0.81[ASN][1000 genomes]
rs364734	0.82[GIH][hapmap]
rs371827	0.89[JPT][hapmap]
rs4708060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708072	1.00[CEU][hapmap]
rs4708073	1.00[CEU][hapmap]
rs473078	0.82[GIH][hapmap]
rs474661	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs479248	1.00[JPT][hapmap]
rs494841	1.00[CEU][hapmap]
rs506157	1.00[CEU][hapmap]
rs516203	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs527606	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs535902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543642	0.82[GIH][hapmap]
rs555840	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs570050	1.00[CEU][hapmap]
rs580531	1.00[CEU][hapmap]
rs583149	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs584078	0.82[CEU][hapmap]
rs584571	1.00[CEU][hapmap]
rs605857	0.81[ASN][1000 genomes]
rs606263	0.81[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs608026	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609790	1.00[CEU][hapmap]
rs609829	1.00[CEU][hapmap]
rs610260	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs611580	1.00[CEU][hapmap]
rs621493	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs625478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs625512	1.00[CEU][hapmap]
rs636166	0.82[GIH][hapmap]
rs636605	1.00[CEU][hapmap]
rs649909	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs654973	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs657212	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs658475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671735	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs674708	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678054	1.00[CEU][hapmap]
rs679272	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685491	1.00[CEU][hapmap]
rs686317	1.00[CEU][hapmap]
rs687210	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs6907936	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs7749897	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764560	1.00[CEU][hapmap]
rs7764983	1.00[CEU][hapmap]
rs780062	1.00[JPT][hapmap]
rs9293930	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs9293933	1.00[CEU][hapmap]
rs9341424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9352000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9352002	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352007	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9360689	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446904	0.93[ASN][1000 genomes]
rs9446952	1.00[CEU][hapmap]
rs9446955	1.00[CEU][hapmap]
rs9446957	1.00[CEU][hapmap]
rs9446964	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs951332	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv830693	chr6:74049342-74216080	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
4	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
7	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
9	esv2763576	chr6:74197638-74277249	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74172200-74229200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:74173800-74206200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:74181800-74214800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:74182400-74206200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr6:74184000-74212000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr6:74187600-74228400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:74192000-74207800	Weak transcription	Psoas Muscle	Psoas
8	chr6:74192000-74214200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:74192000-74225000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:74192200-74226000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:74192400-74225000	Weak transcription	Stomach Mucosa	stomach
12	chr6:74197600-74207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:74197800-74213200	Weak transcription	Fetal Heart	heart
14	chr6:74197800-74225200	Weak transcription	Colonic Mucosa	Colon
15	chr6:74198200-74207400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:74198200-74211200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:74198600-74207600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:74198600-74209600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:74198600-74213800	Weak transcription	Gastric	stomach
20	chr6:74198800-74207000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:74198800-74207200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:74198800-74207200	Weak transcription	HMEC	breast
23	chr6:74198800-74211200	Weak transcription	Aorta	Aorta
24	chr6:74198800-74213000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:74198800-74225000	Weak transcription	Fetal Brain Male	brain
26	chr6:74199000-74207200	Weak transcription	Brain Germinal Matrix	brain
27	chr6:74199000-74207400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:74199000-74224200	Weak transcription	A549	lung
29	chr6:74200000-74206200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:74200000-74212000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:74200000-74215000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:74200000-74215200	Strong transcription	Liver	Liver
33	chr6:74200200-74206000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:74200200-74212800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:74200400-74211800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:74200400-74211800	Strong transcription	Dnd41	blood
37	chr6:74200400-74212000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:74200400-74212200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr6:74200400-74214000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:74200400-74214000	Strong transcription	Fetal Intestine Large	intestine
41	chr6:74200400-74214600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:74200600-74206000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:74200600-74206200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:74200600-74206200	Strong transcription	Adipose Nuclei	Adipose
45	chr6:74200600-74206200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:74200600-74206200	Strong transcription	Placenta	Placenta
47	chr6:74200600-74208200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr6:74200600-74211800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:74200600-74211800	Strong transcription	Left Ventricle	heart
50	chr6:74200600-74212000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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