Variant report

Variant	rs7971538
Chromosome Location	chr12:122473663-122473664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122472899..122475039-chr12:122517716..122519220,2	MCF-7	breast:
2	chr12:122472104..122474450-chr12:122476458..122479458,3	K562	blood:
3	chr12:122450006..122452585-chr12:122472596..122474160,2	K562	blood:
4	chr12:122471870..122474325-chr12:122611041..122613335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175727	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10431199	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840642	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11043216	1.00[JPT][hapmap]
rs11043229	0.81[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs11043237	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11043242	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11043255	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11043263	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11043277	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11043285	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043290	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11043292	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11043295	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829607	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230823	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1610041	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2707058	0.94[CHD][hapmap];1.00[TSI][hapmap]
rs34768683	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3847694	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4069668	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56040016	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56122558	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56142842	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58326739	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59922210	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7137708	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7138296	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7313252	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs73415674	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73415687	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73415696	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958406	1.00[JPT][hapmap]
rs7961660	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978386	0.95[EUR][1000 genomes];1.00[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7971538	HS3ST2	trans	brain	seeQTL
rs7971538	LAMB3	trans	brain	seeQTL
rs7971538	SH3BP1	trans	brain	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122461600-122492400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:122461800-122476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:122462000-122492400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr12:122462200-122474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr12:122462200-122489000	Weak transcription	HUVEC	blood vessel
6	chr12:122462400-122477800	Weak transcription	Fetal Kidney	kidney
7	chr12:122462400-122481800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:122462400-122489000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:122462400-122490400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:122462400-122492200	Weak transcription	Stomach Mucosa	stomach
11	chr12:122462400-122500000	Weak transcription	Hela-S3	cervix
12	chr12:122462600-122478000	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:122466200-122500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:122466400-122489000	Weak transcription	NHLF	lung
15	chr12:122466800-122490200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:122467000-122480600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:122467800-122478000	Strong transcription	Fetal Intestine Small	intestine
18	chr12:122467800-122488800	Weak transcription	Right Atrium	heart
19	chr12:122467800-122500000	Strong transcription	Thymus	Thymus
20	chr12:122467800-122500200	Strong transcription	Dnd41	blood
21	chr12:122468000-122473800	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:122468000-122489200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:122468200-122492800	Weak transcription	NHDF-Ad	bronchial
24	chr12:122468400-122474000	Weak transcription	Ovary	ovary
25	chr12:122468400-122486000	Weak transcription	NH-A	brain
26	chr12:122468400-122489000	Strong transcription	Fetal Stomach	stomach
27	chr12:122468400-122489000	Weak transcription	Psoas Muscle	Psoas
28	chr12:122468600-122478000	Weak transcription	HepG2	liver
29	chr12:122468800-122474000	Weak transcription	HSMM	muscle
30	chr12:122468800-122474800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:122469800-122473800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:122469800-122481800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:122470000-122474200	Weak transcription	A549	lung
34	chr12:122470000-122482600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:122470000-122488800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:122470000-122492400	Strong transcription	Fetal Thymus	thymus
37	chr12:122470000-122492400	Weak transcription	K562	blood
38	chr12:122470200-122478000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:122470600-122488800	Weak transcription	Fetal Heart	heart
40	chr12:122470600-122489800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:122471000-122475000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:122471000-122483000	Weak transcription	GM12878-XiMat	blood
43	chr12:122471200-122474200	Weak transcription	Primary B cells from cord blood	blood
44	chr12:122471600-122473800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr12:122471600-122474000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:122471600-122481800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:122472000-122478000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:122472000-122507200	Weak transcription	Fetal Brain Male	brain
49	chr12:122472400-122481800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:122472400-122484800	Strong transcription	Primary B cells from peripheral blood	blood

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