Variant report

Variant	rs6756918
Chromosome Location	chr2:178487470-178487471
allele	A/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	CTCF	chr2:178487329-178487544	K562	blood:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
2	TAF1	chr2:178487319-178487532	H1-hESC	embryonic stem cell:	n/a	n/a
3	SMC3	chr2:178487304-178487624	HepG2	liver:	n/a	n/a
4	CTCF	chr2:178487400-178487550	HCPEpiC	choroid plexus:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
5	CTCF	chr2:178487380-178487530	SK-N-SH_RA	brain:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
6	CTCF	chr2:178487380-178487530	AoAF	blood vessel:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
7	TAF1	chr2:178487252-178487548	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr2:178487360-178487510	HRE	kidney:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
9	POLR2A	chr2:178487360-178487504	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr2:178487380-178487530	RPTEC	kidney:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
11	CTCF	chr2:178487400-178487550	K562	blood:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
12	RAD21	chr2:178487291-178487626	HepG2	liver:	n/a	n/a
13	CTCF	chr2:178487353-178487545	HepG2	liver:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
14	CTCF	chr2:178487235-178487660	HepG2	liver:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
15	CTCF	chr2:178487360-178487510	HRPEpiC	eye:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
16	CTCF	chr2:178487315-178487578	H1-hESC	embryonic stem cell:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
17	CTCF	chr2:178487360-178487510	HCM	heart:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
18	CEBPB	chr2:178487311-178487604	HepG2	liver:	n/a	n/a
19	CTCF	chr2:178487400-178487550	HepG2	liver:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
20	CTCF	chr2:178487420-178487570	NB4	blood:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
21	TBP	chr2:178487355-178487593	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr2:178487440-178487590	HCT-116	colon:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
23	RAD21	chr2:178487205-178487723	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr2:178487250-178487610	H1-hESC	embryonic stem cell:	n/a	n/a
25	YY1	chr2:178487319-178487542	HCT-116	colon:	n/a	n/a
26	CTCF	chr2:178487362-178487576	ProgFib	skin:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
27	RAD21	chr2:178487309-178487551	K562	blood:	n/a	n/a
28	CTCF	chr2:178487360-178487510	GM12874	blood:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
29	CTCF	chr2:178487369-178487557	Pancreas_OC	pancreas:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
30	CTCF	chr2:178487361-178487560	GM13977	blood:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
31	CTCF	chr2:178487400-178487550	AG04450	lung:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
32	CEBPB	chr2:178487369-178487540	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr2:178487400-178487550	Caco-2	colon:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
34	CTCF	chr2:178487380-178487530	AG09309	skin:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
35	CTCF	chr2:178487408-178487563	Medullo	brain:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
36	CTCF	chr2:178487420-178487570	BJ	skin:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
37	RAD21	chr2:178487385-178487500	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr2:178487360-178487510	GM12867	blood:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
39	CTCF	chr2:178487340-178487490	WERI-Rb-1	eye:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
40	RAD21	chr2:178487213-178487731	HCT-116	colon:	n/a	n/a
41	CTCF	chr2:178487400-178487550	AG04449	skin:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
42	CTCF	chr2:178487340-178487490	HEK293	kidney:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
43	CTCF	chr2:178487320-178487470	GM12872	blood:	n/a	n/a
44	RFX5	chr2:178487405-178487533	HepG2	liver:	n/a	n/a
45	CTCF	chr2:178487400-178487550	HRPEpiC	eye:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
46	CTCF	chr2:178487364-178487565	HepG2	liver:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
47	CTCF	chr2:178487380-178487530	WERI-Rb-1	eye:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
48	CTCF	chr2:178487396-178487538	H1-hESC	embryonic stem cell:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
49	CTCF	chr2:178487340-178487490	SK-N-SH_RA	brain:	n/a	chr2:178487460-178487478 chr2:178487462-178487483
50	CTCF	chr2:178487442-178487490	K562	blood:	n/a	chr2:178487460-178487478 chr2:178487462-178487483

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178485267..178487759-chr2:178497863..178500182,2	K562	blood:
2	chr2:178482307..178483811-chr2:178485382..178487522,2	MCF-7	breast:

Variant related genes	Relation type
TTC30A	TF binding region
ENSG00000197557	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10181259	0.86[CEU][hapmap]
rs10201367	0.95[EUR][1000 genomes]
rs10201883	0.95[EUR][1000 genomes]
rs10497497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497499	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10497504	0.86[CEU][hapmap]
rs10803912	0.84[CEU][hapmap]
rs11679519	0.85[CEU][hapmap]
rs11679730	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11680632	1.00[CHB][hapmap]
rs11694013	0.90[EUR][1000 genomes]
rs11694988	0.92[CEU][hapmap]
rs11889272	0.86[CEU][hapmap]
rs12618150	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12620285	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988366	0.91[CEU][hapmap]
rs13014417	0.84[CEU][hapmap]
rs13017234	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13017429	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs13025391	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13025904	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13026012	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13028757	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1317945	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13431091	0.86[CEU][hapmap]
rs13431105	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1345138	0.86[CEU][hapmap]
rs1348851	0.84[CEU][hapmap]
rs1358326	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1358327	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1374438	0.86[CEU][hapmap]
rs1446839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1527403	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1534305	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544001	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1852530	0.92[CEU][hapmap]
rs1867905	0.86[CEU][hapmap]
rs1918345	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1918346	0.81[EUR][1000 genomes]
rs1997206	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1997207	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2091442	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2178017	0.84[CEU][hapmap]
rs2218575	0.86[CEU][hapmap]
rs2222712	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293475	0.84[CEU][hapmap]
rs2365620	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2365621	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2695315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4110134	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4144278	0.86[CEU][hapmap]
rs4243389	0.86[CEU][hapmap]
rs4341975	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893829	0.84[CEU][hapmap]
rs4893956	0.86[CEU][hapmap]
rs4893967	0.99[EUR][1000 genomes]
rs4893970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893973	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893978	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5025340	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57986285	0.84[EUR][1000 genomes]
rs58160847	0.85[EUR][1000 genomes]
rs6433672	0.84[CEU][hapmap]
rs6433685	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433686	0.86[ASN][1000 genomes]
rs6433687	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433688	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6710109	0.86[CEU][hapmap]
rs6721360	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6723014	0.86[CEU][hapmap]
rs6723031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746233	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7560080	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560514	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560737	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7573345	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7577552	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7578901	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7582179	0.92[CEU][hapmap]
rs7586934	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7588049	0.84[CEU][hapmap]
rs7593744	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7593753	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7597640	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs935426	0.86[CEU][hapmap]
rs941271	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.86[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	esv1815823	chr2:178479149-178489902	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178484000-178499200	Weak transcription	Pancreas	Pancrea
2	chr2:178484200-178487600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:178484200-178487600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:178484200-178487600	Weak transcription	HUVEC	blood vessel
5	chr2:178484200-178490600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:178484200-178490600	Weak transcription	Fetal Stomach	stomach
7	chr2:178484200-178490800	Weak transcription	Right Atrium	heart
8	chr2:178484400-178487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:178484400-178487600	Weak transcription	Liver	Liver
10	chr2:178484400-178490400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:178484400-178490600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:178484400-178490800	Weak transcription	Adipose Nuclei	Adipose
13	chr2:178484400-178490800	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:178485400-178490600	Weak transcription	HepG2	liver
15	chr2:178486800-178488000	Enhancers	Brain Germinal Matrix	brain
16	chr2:178487000-178487800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:178487000-178488000	Enhancers	Fetal Kidney	kidney
18	chr2:178487000-178488400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:178487200-178487600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr2:178487200-178487600	Enhancers	Brain Substantia Nigra	brain
21	chr2:178487200-178487800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr2:178487200-178487800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:178487200-178487800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:178487200-178487800	Enhancers	Brain Anterior Caudate	brain
25	chr2:178487200-178487800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:178487200-178488000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr2:178487200-178488000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:178487400-178487600	Active TSS	Brain Cingulate Gyrus	brain
29	chr2:178487400-178487600	Flanking Active TSS	Psoas Muscle	Psoas
30	chr2:178487400-178487800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:178487400-178487800	Active TSS	Brain Angular Gyrus	brain
32	chr2:178487400-178487800	Active TSS	Brain Hippocampus Middle	brain
33	chr2:178487400-178487800	Enhancers	Fetal Brain Male	brain
34	chr2:178487400-178487800	Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr2:178487400-178488000	Enhancers	Fetal Brain Female	brain

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