Variant report

Variant	rs12038843
Chromosome Location	chr1:62736841-62736842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10157938	0.88[JPT][hapmap]
rs10465842	0.90[JPT][hapmap]
rs10493318	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10889318	0.90[JPT][hapmap]
rs11207955	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11207956	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12031172	0.87[ASN][1000 genomes]
rs12031176	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12043263	0.86[ASN][1000 genomes]
rs12123763	0.87[ASN][1000 genomes]
rs12127630	0.92[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12138544	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1555832	0.90[ASN][1000 genomes]
rs17123603	1.00[ASW][hapmap]
rs17855078	0.93[ASN][1000 genomes]
rs1886834	0.90[JPT][hapmap]
rs1925827	0.86[JPT][hapmap]
rs2666509	0.90[JPT][hapmap]
rs2765266	0.90[JPT][hapmap]
rs2765268	0.90[JPT][hapmap]
rs2765269	0.90[JPT][hapmap]
rs34477066	0.87[ASN][1000 genomes]
rs3850629	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs3861936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4915606	0.90[JPT][hapmap]
rs4915607	0.90[JPT][hapmap]
rs6675508	0.90[JPT][hapmap]
rs881548	0.90[JPT][hapmap]
rs927777	0.84[CHB][hapmap]
rs958802	0.92[CHB][hapmap]
rs9803815	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9804022	0.87[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12038843	KANK4	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:62729000-62737600	Weak transcription	Right Atrium	heart
4	chr1:62729600-62737400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:62729600-62737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:62729600-62737600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:62729600-62737800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:62729800-62737400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:62732200-62737000	Weak transcription	Esophagus	oesophagus
10	chr1:62732200-62737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:62732400-62737000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:62732400-62737400	Weak transcription	Fetal Kidney	kidney
13	chr1:62732400-62737600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:62732400-62737600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:62732400-62737600	Weak transcription	Placenta	Placenta
16	chr1:62732400-62740000	Weak transcription	Liver	Liver
17	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:62732800-62737600	Weak transcription	Fetal Intestine Small	intestine
19	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
20	chr1:62733200-62737400	Weak transcription	Fetal Lung	lung
21	chr1:62734000-62737400	Weak transcription	Adipose Nuclei	Adipose
22	chr1:62734200-62750800	Weak transcription	Gastric	stomach
23	chr1:62734800-62737400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:62734800-62737400	Weak transcription	Pancreas	Pancrea
25	chr1:62734800-62737600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:62735800-62740600	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr1:62736000-62737000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:62736200-62739600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:62736400-62738400	Enhancers	Fetal Heart	heart
30	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:62736400-62739400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:62736400-62740400	Enhancers	Fetal Thymus	thymus
33	chr1:62736400-62741000	Strong transcription	HepG2	liver
34	chr1:62736800-62737000	Enhancers	Fetal Muscle Trunk	muscle
35	chr1:62736800-62737200	Enhancers	Fetal Stomach	stomach
36	chr1:62736800-62737400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:62736800-62738400	Enhancers	Fetal Muscle Leg	muscle
38	chr1:62736800-62738800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr1:62736800-62739000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:62736800-62739000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr1:62736800-62739400	Enhancers	Primary T cells from cord blood	blood
42	chr1:62736800-62739600	Enhancers	Primary T cells fromperipheralblood	blood
43	chr1:62736800-62739600	Enhancers	Primary T helper cells PMA-I stimulated	--

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