Variant report

Variant	rs12989231
Chromosome Location	chr2:98629966-98629967
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98615869..98618300-chr2:98627812..98630774,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12612060	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466156	1.00[CHB][hapmap]
rs2122755	1.00[CHB][hapmap]
rs298904	0.81[MEX][hapmap]
rs298906	0.81[MEX][hapmap]
rs4851915	1.00[CHB][hapmap]
rs67425556	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12989231	INPP4A	cis	parietal	SCAN
rs12989231	MRPL30	cis	cerebellum	SCAN
rs12989231	AFF3	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98613800-98636200	Weak transcription	Stomach Mucosa	stomach
2	chr2:98620200-98637800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:98622600-98641800	Weak transcription	Gastric	stomach
4	chr2:98626400-98634000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:98626600-98630200	Enhancers	Fetal Muscle Leg	muscle
6	chr2:98627000-98630200	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr2:98627200-98630000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:98627200-98630200	Weak transcription	Pancreas	Pancrea
9	chr2:98627400-98630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:98627400-98641600	Weak transcription	Psoas Muscle	Psoas
11	chr2:98627800-98630000	Weak transcription	Ovary	ovary
12	chr2:98627800-98630200	Weak transcription	Left Ventricle	heart
13	chr2:98628000-98631000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:98629000-98630000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:98629000-98630000	Enhancers	Duodenum Mucosa	Duodenum
16	chr2:98629200-98630200	Weak transcription	Colonic Mucosa	Colon
17	chr2:98629200-98633400	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:98629400-98633400	Enhancers	Primary B cells from cord blood	blood
19	chr2:98629600-98630000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr2:98629600-98630800	Flanking Active TSS	GM12878-XiMat	blood
21	chr2:98629800-98630000	Flanking Active TSS	HepG2	liver
22	chr2:98629800-98630000	Enhancers	NH-A	brain
23	chr2:98629800-98630400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:98629800-98630400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:98629800-98630400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:98629800-98630400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr2:98629800-98630600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:98629800-98630600	Enhancers	HSMM	muscle
29	chr2:98629800-98630600	Flanking Active TSS	Osteobl	bone

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