Variant report

Variant	rs2271478
Chromosome Location	chr12:39695139-39695140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39694207..39696152-chr12:39837237..39840087,2	K562	blood:
2	chr12:39690972..39693239-chr12:39694761..39697625,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11172144	1.00[JPT][hapmap]
rs11172162	1.00[JPT][hapmap]
rs11172480	0.92[AMR][1000 genomes]
rs12228013	1.00[JPT][hapmap]
rs1512941	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1512943	0.90[ASN][1000 genomes]
rs17126997	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17127029	0.83[ASN][1000 genomes]
rs17127070	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17127094	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs17127100	0.83[ASN][1000 genomes]
rs17127129	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17127138	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2137495	0.83[ASN][1000 genomes]
rs2292491	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4620763	0.86[ASN][1000 genomes]
rs57196300	0.83[ASN][1000 genomes]
rs59967849	0.83[ASN][1000 genomes]
rs7135918	0.83[ASN][1000 genomes]
rs7307730	0.86[ASN][1000 genomes]
rs7308138	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73086885	0.83[ASN][1000 genomes]
rs7956823	0.88[ASN][1000 genomes]
rs7966841	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7970819	0.83[ASN][1000 genomes]
rs7976275	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7978854	0.83[ASN][1000 genomes]
rs7980595	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7980857	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs963637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899013	chr12:39567945-39732430	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470286	chr12:39651893-39729700	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2271478	KIF21A	cis	multi-tissue	Pritchard
rs2271478	ABCD2	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39682000-39699200	Weak transcription	Hela-S3	cervix
2	chr12:39683200-39696000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:39684400-39695400	Weak transcription	A549	lung
4	chr12:39685200-39697400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:39685200-39714400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:39686400-39699600	Weak transcription	HMEC	breast
7	chr12:39686600-39722400	Weak transcription	GM12878-XiMat	blood
8	chr12:39686600-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:39686800-39729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:39686800-39738800	Weak transcription	Pancreas	Pancrea
11	chr12:39687200-39696800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:39687200-39726400	Weak transcription	Fetal Intestine Small	intestine
13	chr12:39687600-39723800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:39688400-39709800	Weak transcription	Ovary	ovary
15	chr12:39688400-39724600	Weak transcription	Esophagus	oesophagus
16	chr12:39688400-39726400	Weak transcription	Aorta	Aorta
17	chr12:39688800-39695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr12:39688800-39696800	Weak transcription	Brain Anterior Caudate	brain
19	chr12:39688800-39697200	Weak transcription	Left Ventricle	heart
20	chr12:39688800-39698200	Weak transcription	Brain Substantia Nigra	brain
21	chr12:39689000-39695600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:39689000-39697800	Weak transcription	Brain Angular Gyrus	brain
23	chr12:39689000-39698400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:39689000-39699600	Weak transcription	Fetal Heart	heart
25	chr12:39689000-39724000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:39689400-39695400	Weak transcription	Fetal Brain Female	brain
27	chr12:39689400-39695800	Weak transcription	K562	blood
28	chr12:39689400-39696400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:39689600-39696400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:39689600-39699000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:39689600-39702200	Weak transcription	Right Ventricle	heart
32	chr12:39689600-39725400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:39690400-39696200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:39690400-39703000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:39690400-39715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:39690600-39701400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:39690600-39711600	Weak transcription	Placenta	Placenta
38	chr12:39690800-39697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:39690800-39700800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:39690800-39704400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:39691800-39703400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:39692200-39696800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:39692200-39697200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:39692400-39697800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:39692600-39697000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:39693800-39705600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:39694000-39695200	Strong transcription	Liver	Liver
48	chr12:39694000-39696000	Enhancers	Brain Germinal Matrix	brain
49	chr12:39694000-39697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:39694000-39699800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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