Variant report

Variant	rs12477252
Chromosome Location	chr2:39004858-39004859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
2	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
3	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
4	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
5	chr2:39004566..39006965-chr2:39038166..39040437,2	MCF-7	breast:
6	chr2:38983494..38986054-chr2:39002724..39005182,2	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000223922	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10168789	0.82[ASN][1000 genomes]
rs10173118	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173240	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10197412	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10865143	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865144	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11694383	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11889280	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12465043	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12468732	0.95[ASN][1000 genomes]
rs12469681	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472454	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12473036	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618118	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12712621	0.93[ASN][1000 genomes]
rs12712622	0.87[ASN][1000 genomes]
rs12991609	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12996194	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13011522	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13014136	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029406	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13383541	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13411868	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417196	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530852	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530853	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979142	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2037875	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3099952	0.88[ASN][1000 genomes]
rs3099960	0.85[ASN][1000 genomes]
rs3099965	0.94[EUR][1000 genomes]
rs3099984	0.84[ASN][1000 genomes]
rs3099985	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3099987	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3099988	0.86[ASN][1000 genomes]
rs3099989	0.86[ASN][1000 genomes]
rs3099991	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3112140	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112149	0.85[ASN][1000 genomes]
rs3112198	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3112200	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112205	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112209	0.81[ASN][1000 genomes]
rs3112210	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112216	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3770681	0.84[ASN][1000 genomes]
rs4602206	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4630748	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4670894	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4670897	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56393601	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60012208	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62144837	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544175	0.84[ASN][1000 genomes]
rs6715866	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6723868	0.88[ASN][1000 genomes]
rs6753251	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7419616	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7419838	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7588621	0.84[ASN][1000 genomes]
rs7589162	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12477252	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:39004200-39005000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:39004400-39006200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:39004600-39005000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:39004600-39005000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:39004600-39005000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:39004600-39005000	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr2:39004600-39005800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:39004600-39005800	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr2:39004600-39005800	Active TSS	Brain Germinal Matrix	brain
11	chr2:39004600-39005800	Active TSS	Brain Substantia Nigra	brain
12	chr2:39004600-39005800	Active TSS	Duodenum Mucosa	Duodenum
13	chr2:39004600-39006000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:39004600-39006600	Active TSS	A549	lung
15	chr2:39004800-39005000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:39004800-39005000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr2:39004800-39005000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr2:39004800-39005000	Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr2:39004800-39005000	Flanking Active TSS	Primary B cells from peripheral blood	blood
20	chr2:39004800-39005000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:39004800-39005000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr2:39004800-39005000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:39004800-39005000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr2:39004800-39005000	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr2:39004800-39005200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
26	chr2:39004800-39005200	Active TSS	HepG2	liver
27	chr2:39004800-39005400	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr2:39004800-39005400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr2:39004800-39005400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:39004800-39005400	Active TSS	Fetal Thymus	thymus
31	chr2:39004800-39005400	Active TSS	Osteobl	bone
32	chr2:39004800-39005600	Active TSS	Primary T cells from cord blood	blood
33	chr2:39004800-39005600	Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr2:39004800-39005600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:39004800-39005600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:39004800-39005600	Active TSS	Adipose Nuclei	Adipose
37	chr2:39004800-39005600	Active TSS	Liver	Liver
38	chr2:39004800-39005600	Active TSS	Stomach Smooth Muscle	stomach
39	chr2:39004800-39005600	Active TSS	Dnd41	blood
40	chr2:39004800-39005600	Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:39004800-39005800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr2:39004800-39005800	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr2:39004800-39005800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:39004800-39005800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:39004800-39005800	Active TSS	Brain Anterior Caudate	brain
46	chr2:39004800-39005800	Active TSS	Brain Cingulate Gyrus	brain
47	chr2:39004800-39005800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr2:39004800-39005800	Active TSS	Fetal Brain Female	brain
49	chr2:39004800-39005800	Active TSS	Placenta	Placenta
50	chr2:39004800-39005800	Active TSS	Rectal Mucosa Donor 29	rectum

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