Variant report

Variant	rs7978354
Chromosome Location	chr12:66706748-66706749
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66704984..66707430-chr12:66740010..66742020,2	K562	blood:
2	chr12:66705829..66707334-chr12:66713172..66714827,2	K562	blood:
3	chr12:65563343..65564912-chr12:66705343..66707432,2	MCF-7	breast:
4	chr12:66705611..66708293-chr12:66712506..66715212,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174106	Chromatin interaction
ENSG00000127311	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10748038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748039	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784521	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784524	1.00[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10878403	0.86[CHB][hapmap]
rs11176137	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11176138	0.87[CEU][hapmap];0.99[EUR][1000 genomes]
rs11176139	0.95[EUR][1000 genomes]
rs11176142	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs11176144	0.89[EUR][1000 genomes]
rs12367438	0.90[EUR][1000 genomes]
rs12816200	0.90[EUR][1000 genomes]
rs1495495	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1898305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1971302	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2118139	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3741603	0.94[CEU][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4382951	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4554930	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581676	0.94[CEU][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7132724	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs7133479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298868	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7315366	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7316880	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956960	0.98[EUR][1000 genomes]
rs7957877	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7959466	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969887	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7973358	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS 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 miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7978354	HELB	cis	parietal	SCAN
rs7978354	HELB	Cis_1M	lymphoblastoid	RTeQTL
rs7978354	HELB	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66696800-66714800	Weak transcription	NHDF-Ad	bronchial
2	chr12:66696800-66716600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:66696800-66717600	Weak transcription	Fetal Brain Male	brain
4	chr12:66696800-66719600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:66696800-66723600	Weak transcription	HSMM	muscle
6	chr12:66696800-66734200	Weak transcription	HSMMtube	muscle
7	chr12:66697000-66725000	Weak transcription	Ovary	ovary
8	chr12:66697200-66707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:66697200-66716000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:66697200-66725600	Weak transcription	Fetal Heart	heart
11	chr12:66697200-66733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:66697200-66734800	Weak transcription	Esophagus	oesophagus
13	chr12:66697200-66735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:66697400-66707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:66697400-66714800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:66697400-66719800	Weak transcription	Psoas Muscle	Psoas
18	chr12:66697400-66724800	Weak transcription	Pancreas	Pancrea
19	chr12:66697400-66732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:66697400-66732400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:66697400-66735000	Weak transcription	Right Ventricle	heart
22	chr12:66697600-66714600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:66697800-66725000	Weak transcription	Colonic Mucosa	Colon
24	chr12:66698200-66707400	Weak transcription	Small Intestine	intestine
25	chr12:66698200-66707600	Weak transcription	Brain Hippocampus Middle	brain
26	chr12:66698200-66725200	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:66698200-66735000	Weak transcription	Fetal Brain Female	brain
28	chr12:66698400-66706800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:66698400-66713000	Weak transcription	Brain Substantia Nigra	brain
30	chr12:66698400-66714800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:66698400-66732400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:66698400-66734800	Weak transcription	HepG2	liver
33	chr12:66698600-66714800	Weak transcription	Thymus	Thymus
34	chr12:66699000-66708600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr12:66699000-66735000	Weak transcription	K562	blood
36	chr12:66699400-66709800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr12:66700600-66710000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:66702400-66724800	Weak transcription	Aorta	Aorta
39	chr12:66702600-66734800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:66703400-66713800	Strong transcription	Primary B cells from cord blood	blood
41	chr12:66704200-66709200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:66704200-66712600	Weak transcription	Brain Angular Gyrus	brain
43	chr12:66704200-66725600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:66704200-66733600	Weak transcription	A549	lung
45	chr12:66704200-66735000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr12:66704400-66709800	Weak transcription	Fetal Lung	lung
47	chr12:66704400-66724800	Weak transcription	Lung	lung
48	chr12:66704400-66732200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:66704400-66733600	Weak transcription	Brain Anterior Caudate	brain
50	chr12:66704400-66741800	Weak transcription	Hela-S3	cervix

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