Variant report

Variant	rs10784369
Chromosome Location	chr12:40494129-40494130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:40481786..40484578-chr12:40492831..40495668,2	MCF-7	breast:
2	12:40491106-40496076..12:40793507-40812339	GM12878	blood:
3	chr12:40480723..40487168-chr12:40489659..40495663,7	K562	blood:
4	chr12:40490927..40494840-chr12:40498273..40501299,7	MCF-7	breast:
5	chr12:40485743..40487373-chr12:40492578..40494956,2	MCF-7	breast:
6	chr12:40419862..40422582-chr12:40493466..40495715,2	K562	blood:
7	12:40491106-40496076..12:40703633-40711447	GM12878	blood:
8	chr12:40484990..40487793-chr12:40489552..40494427,5	K562	blood:

Variant related genes	Relation type
ENSG00000205592	Chromatin interaction
ENSG00000151229	Chromatin interaction
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1005956	0.83[JPT][hapmap]
rs10506140	0.83[JPT][hapmap]
rs10747971	0.92[JPT][hapmap]
rs10747989	0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs10784338	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10784353	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10784356	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784359	0.82[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs10877891	0.92[JPT][hapmap]
rs10877990	0.94[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10878031	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878049	0.89[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs10878089	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174609	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs11174670	0.81[ASN][1000 genomes]
rs11175024	0.82[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12813098	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12823555	0.85[CEU][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1482281	0.92[JPT][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs1586038	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1600866	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1813122	0.92[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2128277	0.92[JPT][hapmap]
rs2404352	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2896825	0.92[JPT][hapmap]
rs2896905	0.82[ASW][hapmap];0.84[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs3925535	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4625545	0.83[JPT][hapmap]
rs4767960	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768200	0.90[JPT][hapmap]
rs4768204	0.83[JPT][hapmap]
rs530602	0.92[JPT][hapmap]
rs550669	0.92[JPT][hapmap]
rs6581504	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6650226	0.92[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs716268	0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7313209	0.92[JPT][hapmap]
rs7313231	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs7953129	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7954875	0.81[ASN][1000 genomes]
rs7959498	0.92[JPT][hapmap]
rs7960662	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964150	0.92[JPT][hapmap]
rs7970812	0.92[JPT][hapmap]
rs9669240	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.84[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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1816874	chr12:40492814-40499934	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
5	esv1822895	chr12:40492814-40499934	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
6	esv1838004	chr12:40492814-40499934	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
7	esv1841992	chr12:40492814-40499934	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
8	esv1850635	chr12:40492814-40499934	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
9	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv1839896	chr12:40493591-40499908	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10784369	KIF21A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40466400-40498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40471400-40496800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:40474400-40497000	Weak transcription	Ovary	ovary
4	chr12:40475400-40497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:40475600-40496400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:40476400-40497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:40476600-40498400	Weak transcription	Fetal Stomach	stomach
8	chr12:40476800-40497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:40477000-40497000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:40477200-40495200	Weak transcription	Hela-S3	cervix
11	chr12:40477400-40496800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:40480600-40496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:40482000-40497800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:40485600-40496800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:40487000-40497400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr12:40488200-40498600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:40491000-40497000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:40492000-40494600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr12:40492000-40495400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:40492400-40498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:40492600-40494400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr12:40492600-40494600	Enhancers	Fetal Intestine Large	intestine
23	chr12:40492600-40494600	Enhancers	Stomach Mucosa	stomach
24	chr12:40492800-40494200	Enhancers	Brain Hippocampus Middle	brain
25	chr12:40492800-40494200	Enhancers	Fetal Intestine Small	intestine
26	chr12:40492800-40494400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:40492800-40496800	Weak transcription	Pancreas	Pancrea
28	chr12:40492800-40497600	Weak transcription	Left Ventricle	heart
29	chr12:40492800-40498000	Weak transcription	Gastric	stomach
30	chr12:40492800-40498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:40492800-40498600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:40492800-40498600	Weak transcription	Lung	lung
33	chr12:40493000-40494200	Flanking Active TSS	K562	blood
34	chr12:40493000-40496600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:40493200-40494200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:40493200-40494200	Enhancers	A549	lung
37	chr12:40493400-40494200	Enhancers	Brain Cingulate Gyrus	brain
38	chr12:40493400-40494200	Enhancers	Fetal Lung	lung
39	chr12:40493400-40494400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:40493400-40494400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:40493400-40495400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:40493600-40494200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:40493600-40495800	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:40493600-40496800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:40493600-40497000	Weak transcription	Brain Anterior Caudate	brain
46	chr12:40493600-40497000	Weak transcription	Fetal Kidney	kidney
47	chr12:40493800-40497400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:40493800-40497400	Weak transcription	Fetal Heart	heart
49	chr12:40494000-40495200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:40494000-40496800	Weak transcription	Duodenum Mucosa	Duodenum

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