Variant report

Variant	rs1168308
Chromosome Location	chr12:66742183-66742184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66741405..66742323-chrX:137857357..137858289,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1027399	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1027400	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1027401	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1039056	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1060724	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784525	0.89[EUR][1000 genomes]
rs1168290	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168291	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168292	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168293	0.97[EUR][1000 genomes]
rs1168294	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168295	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168296	0.98[EUR][1000 genomes]
rs1168297	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168298	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168299	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168300	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168301	0.98[EUR][1000 genomes]
rs1168302	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168303	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168304	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168305	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168306	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168307	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168309	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168310	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1168311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168314	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168315	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168316	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168317	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168318	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168319	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168320	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168321	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168322	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168325	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168330	0.93[EUR][1000 genomes]
rs1168332	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168333	0.95[EUR][1000 genomes]
rs1168334	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168338	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168339	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168340	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168341	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168342	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168343	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168344	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168345	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168346	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168347	0.95[EUR][1000 genomes]
rs1168348	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168351	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168352	0.98[EUR][1000 genomes]
rs1168353	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168356	0.98[EUR][1000 genomes]
rs1168357	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168358	0.98[EUR][1000 genomes]
rs1177555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1179889	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1183272	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1183274	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1184551	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1184552	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1185244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1495497	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1625394	0.84[CEU][hapmap]
rs1795527	0.87[EUR][1000 genomes]
rs1795529	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2172881	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2951656	0.96[EUR][1000 genomes]
rs4762091	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61925898	0.84[EUR][1000 genomes]
rs6581677	0.92[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581678	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs903587	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903589	0.98[EUR][1000 genomes]
rs903590	0.98[EUR][1000 genomes]
rs961049	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1168308	HELB	cis	parietal	SCAN
rs1168308	HELB	cis	cerebellum	SCAN
rs1168308	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:66710200-66792800	Weak transcription	Fetal Kidney	kidney
3	chr12:66724200-66745400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:66725400-66746400	Weak transcription	Small Intestine	intestine
5	chr12:66725600-66742800	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:66735000-66751200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:66735200-66742200	Weak transcription	Fetal Thymus	thymus
8	chr12:66735600-66742800	Weak transcription	Placenta	Placenta
9	chr12:66735600-66745800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:66735600-66747600	Weak transcription	Gastric	stomach
11	chr12:66735600-66751400	Weak transcription	Esophagus	oesophagus
12	chr12:66735600-66752800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:66735600-66755000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:66735800-66742200	Weak transcription	Liver	Liver
15	chr12:66735800-66747200	Weak transcription	Colonic Mucosa	Colon
16	chr12:66735800-66749800	Weak transcription	Spleen	Spleen
17	chr12:66735800-66750400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:66735800-66751000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:66735800-66754600	Weak transcription	Adipose Nuclei	Adipose
20	chr12:66735800-66759800	Weak transcription	Thymus	Thymus
21	chr12:66736000-66742200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:66736000-66742200	Weak transcription	GM12878-XiMat	blood
23	chr12:66736000-66744400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:66736000-66744400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:66736000-66746600	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:66736000-66751000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:66736000-66766400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:66736200-66745600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:66736200-66746600	Weak transcription	Fetal Lung	lung
30	chr12:66736400-66742200	Weak transcription	Fetal Intestine Large	intestine
31	chr12:66736400-66745800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:66736600-66759600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:66736800-66744400	Weak transcription	Left Ventricle	heart
34	chr12:66737000-66744000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:66737200-66742800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:66737200-66746000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:66737200-66746600	Weak transcription	Pancreas	Pancrea
38	chr12:66737200-66748000	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:66737200-66749200	Weak transcription	Lung	lung
40	chr12:66737200-66751000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:66737400-66742600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:66737400-66743400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:66737400-66743600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:66737400-66756600	Weak transcription	Aorta	Aorta
45	chr12:66738000-66792800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr12:66738200-66744200	Weak transcription	A549	lung
47	chr12:66738200-66744800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:66738200-66770400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr12:66738800-66742200	Weak transcription	Dnd41	blood
50	chr12:66738800-66770400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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