Variant report

Variant	rs12440982
Chromosome Location	chr15:99717079-99717080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr15:99717021-99717367	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr15:99716892-99717434	SK-N-SH	brain:	n/a	chr15:99717203-99717210
3	GATA3	chr15:99716796-99718001	SK-N-SH	brain:	n/a	chr15:99717794-99717807
4	GATA2	chr15:99716969-99717426	SH-SY5Y	brain:	n/a	n/a
5	GATA3	chr15:99716862-99717123	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99715590..99718569-chr15:99720047..99722530,2	K562	blood:

Variant related genes	Relation type
TTC23	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11247070	0.84[CHB][hapmap]
rs11247071	0.89[CHB][hapmap]
rs11247076	0.88[CHB][hapmap]
rs11247077	0.89[CHB][hapmap]
rs11247078	0.89[CHB][hapmap]
rs12439693	0.84[CHB][hapmap]
rs12439819	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs12439820	0.89[CHB][hapmap]
rs12440477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440640	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441965	0.89[CHB][hapmap]
rs12441996	0.89[CHB][hapmap]
rs12442235	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12592097	0.80[CHB][hapmap]
rs12593076	0.89[CHB][hapmap]
rs12594250	0.89[CHB][hapmap]
rs12594607	0.89[CHB][hapmap]
rs12594709	0.82[CHB][hapmap]
rs12595099	0.84[CHB][hapmap]
rs12901547	0.89[CHB][hapmap]
rs12902590	0.89[CHB][hapmap]
rs12906323	0.88[CHB][hapmap]
rs12906924	0.89[CHB][hapmap]
rs12907938	0.89[CHB][hapmap]
rs12914665	0.89[CHB][hapmap]
rs1510058	0.84[CHB][hapmap]
rs1612365	0.89[CHB][hapmap]
rs1670229	0.88[CHB][hapmap]
rs1876741	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2006670	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2048303	0.88[CHB][hapmap]
rs2048304	0.82[CHB][hapmap]
rs2089708	0.89[CHB][hapmap]
rs2136629	0.84[CHB][hapmap]
rs2290352	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2623182	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2861371	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3134588	0.85[JPT][hapmap]
rs3759903	0.89[CHB][hapmap]
rs3784602	0.83[CHB][hapmap]
rs3961782	0.89[CHB][hapmap]
rs4965215	0.85[ASN][1000 genomes]
rs4965216	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4965446	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs4965448	0.87[ASN][1000 genomes]
rs4965451	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58627039	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58653169	0.96[ASN][1000 genomes]
rs7163435	0.89[CHB][hapmap]
rs7169355	0.89[CHB][hapmap]
rs7170952	0.89[CHB][hapmap]
rs7172501	0.85[CHB][hapmap]
rs7178606	0.89[CHB][hapmap]
rs73480175	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73480191	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8031904	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
9	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
15	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS 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	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:99694800-99721200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:99694800-99732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:99694800-99732600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:99695200-99721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:99695200-99721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:99695200-99732400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
11	chr15:99699400-99731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:99700200-99731200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:99700400-99730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:99703400-99728200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:99705000-99732400	Weak transcription	Fetal Kidney	kidney
16	chr15:99707800-99717200	Weak transcription	HUVEC	blood vessel
17	chr15:99709400-99732600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr15:99709600-99731400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:99709600-99732600	Weak transcription	GM12878-XiMat	blood
20	chr15:99709800-99732600	Weak transcription	Spleen	Spleen
21	chr15:99710000-99719600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:99710000-99721000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:99710200-99724000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:99710400-99732400	Weak transcription	Fetal Brain Female	brain
25	chr15:99711200-99720000	Weak transcription	Brain Anterior Caudate	brain
26	chr15:99711400-99730800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:99711600-99717600	Weak transcription	HMEC	breast
28	chr15:99711600-99721400	Weak transcription	NHLF	lung
29	chr15:99711600-99725000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:99711600-99738600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:99711800-99732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:99712200-99717200	Strong transcription	Fetal Intestine Small	intestine
33	chr15:99712800-99731600	Weak transcription	Colonic Mucosa	Colon
34	chr15:99713600-99720000	Weak transcription	HepG2	liver
35	chr15:99713600-99721000	Weak transcription	A549	lung
36	chr15:99713800-99718000	Enhancers	Rectal Smooth Muscle	rectum
37	chr15:99714000-99720400	Weak transcription	HSMMtube	muscle
38	chr15:99714400-99721600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:99714400-99724000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:99714400-99725000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:99714600-99721600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:99715000-99719200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:99715000-99721800	Weak transcription	Osteobl	bone
44	chr15:99715200-99717200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:99715200-99717400	Enhancers	Psoas Muscle	Psoas
46	chr15:99715200-99725600	Weak transcription	NH-A	brain
47	chr15:99715400-99717200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:99715400-99717200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:99715400-99717400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr15:99715400-99717400	Enhancers	Left Ventricle	heart

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