Variant report

Variant	rs903589
Chromosome Location	chr12:66745835-66745836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66743145..66746019-chr12:66747727..66750214,3	K562	blood:
2	chr12:66745711..66746634-chr12:67087184..67088269,6	MCF-7	breast:
3	chr12:66745697..66746293-chr12:67082336..67083172,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1027399	0.92[EUR][1000 genomes]
rs1027400	0.94[EUR][1000 genomes]
rs1027401	0.95[EUR][1000 genomes]
rs1039056	0.96[EUR][1000 genomes]
rs1060724	0.97[EUR][1000 genomes]
rs10784525	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168290	0.92[EUR][1000 genomes]
rs1168291	0.97[EUR][1000 genomes]
rs1168292	0.98[EUR][1000 genomes]
rs1168293	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168294	0.97[EUR][1000 genomes]
rs1168295	0.95[EUR][1000 genomes]
rs1168296	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168297	0.96[EUR][1000 genomes]
rs1168298	0.97[EUR][1000 genomes]
rs1168299	0.96[EUR][1000 genomes]
rs1168300	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs1168301	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168302	0.95[EUR][1000 genomes]
rs1168303	0.97[EUR][1000 genomes]
rs1168304	0.97[EUR][1000 genomes]
rs1168305	0.97[EUR][1000 genomes]
rs1168306	0.98[EUR][1000 genomes]
rs1168307	0.95[EUR][1000 genomes]
rs1168308	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[EUR][1000 genomes]
rs1168309	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[EUR][1000 genomes]
rs1168310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168311	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[EUR][1000 genomes]
rs1168314	0.97[EUR][1000 genomes]
rs1168315	0.97[EUR][1000 genomes]
rs1168316	0.97[EUR][1000 genomes]
rs1168317	0.97[EUR][1000 genomes]
rs1168318	0.99[EUR][1000 genomes]
rs1168319	0.97[EUR][1000 genomes]
rs1168320	0.97[EUR][1000 genomes]
rs1168321	0.97[EUR][1000 genomes]
rs1168322	0.97[EUR][1000 genomes]
rs1168325	0.93[EUR][1000 genomes]
rs1168327	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[EUR][1000 genomes]
rs1168328	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[EUR][1000 genomes]
rs1168329	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[EUR][1000 genomes]
rs1168330	0.93[EUR][1000 genomes]
rs1168332	0.95[EUR][1000 genomes]
rs1168333	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1168334	0.95[EUR][1000 genomes]
rs1168338	0.92[EUR][1000 genomes]
rs1168339	0.92[EUR][1000 genomes]
rs1168340	0.92[EUR][1000 genomes]
rs1168341	0.93[EUR][1000 genomes]
rs1168342	0.93[EUR][1000 genomes]
rs1168343	0.97[EUR][1000 genomes]
rs1168344	0.97[EUR][1000 genomes]
rs1168345	0.96[EUR][1000 genomes]
rs1168346	0.97[EUR][1000 genomes]
rs1168347	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168348	0.94[EUR][1000 genomes]
rs1168351	0.96[EUR][1000 genomes]
rs1168352	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168353	0.96[EUR][1000 genomes]
rs1168356	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168357	0.97[EUR][1000 genomes]
rs1168358	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1177555	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1179889	0.86[EUR][1000 genomes]
rs1183272	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1183274	0.96[EUR][1000 genomes]
rs1184551	0.93[EUR][1000 genomes]
rs1184552	0.88[EUR][1000 genomes]
rs1185244	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1495497	0.93[EUR][1000 genomes]
rs1625394	0.85[CEU][hapmap]
rs1795527	0.86[EUR][1000 genomes]
rs1795529	0.91[EUR][1000 genomes]
rs2172881	0.90[EUR][1000 genomes]
rs2951656	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4762091	0.97[EUR][1000 genomes]
rs61925898	0.84[EUR][1000 genomes]
rs6581677	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs6581678	0.87[EUR][1000 genomes]
rs903587	0.97[EUR][1000 genomes]
rs903590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961049	0.93[AFR][1000 genomes];0.96[EUR][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	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs903589	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66710200-66792800	Weak transcription	Fetal Kidney	kidney
2	chr12:66725400-66746400	Weak transcription	Small Intestine	intestine
3	chr12:66735000-66751200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:66735600-66747600	Weak transcription	Gastric	stomach
5	chr12:66735600-66751400	Weak transcription	Esophagus	oesophagus
6	chr12:66735600-66752800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:66735600-66755000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:66735800-66747200	Weak transcription	Colonic Mucosa	Colon
9	chr12:66735800-66749800	Weak transcription	Spleen	Spleen
10	chr12:66735800-66750400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:66735800-66751000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:66735800-66754600	Weak transcription	Adipose Nuclei	Adipose
13	chr12:66735800-66759800	Weak transcription	Thymus	Thymus
14	chr12:66736000-66746600	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:66736000-66751000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:66736000-66766400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:66736200-66746600	Weak transcription	Fetal Lung	lung
18	chr12:66736600-66759600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:66737200-66746000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:66737200-66746600	Weak transcription	Pancreas	Pancrea
21	chr12:66737200-66748000	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:66737200-66749200	Weak transcription	Lung	lung
23	chr12:66737200-66751000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:66737400-66756600	Weak transcription	Aorta	Aorta
25	chr12:66738000-66792800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:66738200-66770400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:66738800-66770400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:66739200-66746200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:66739200-66747400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:66739200-66758600	Weak transcription	Fetal Intestine Small	intestine
31	chr12:66739400-66746400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr12:66739400-66747800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:66739400-66765800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:66739400-66766200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:66740000-66748600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:66740600-66746800	Weak transcription	Brain Anterior Caudate	brain
37	chr12:66740600-66747800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:66740800-66748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:66742200-66749000	Strong transcription	Primary T cells from cord blood	blood
40	chr12:66742600-66746000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:66743000-66787600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:66743200-66763400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:66743200-66763800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:66743400-66746000	Weak transcription	Brain Germinal Matrix	brain
45	chr12:66743400-66749600	Weak transcription	Placenta	Placenta
46	chr12:66743400-66761600	Weak transcription	Colon Smooth Muscle	Colon
47	chr12:66743600-66764000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:66744000-66755200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:66744400-66746200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:66744400-66747600	Weak transcription	Fetal Stomach	stomach

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