Variant report

Variant	rs3010297
Chromosome Location	chr6:139794302-139794303
allele	A/G
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	POLR2A	chr6:139794033-139794988	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:139794161-139795273	SK-N-MC	brain:	n/a	n/a
3	TBL1XR1	chr6:139794255-139794407	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000238099	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17406820	0.81[CHD][hapmap]
rs62440875	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518835	chr6:139770067-139800892	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3010297	KIAA1244	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139789800-139794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:139789800-139794400	Weak transcription	HMEC	breast
3	chr6:139789800-139794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:139790000-139794400	Weak transcription	Fetal Heart	heart
5	chr6:139790000-139795000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:139791600-139794400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:139793400-139795400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr6:139793600-139794400	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr6:139793600-139794400	Enhancers	Pancreas	Pancrea
10	chr6:139793600-139794600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:139793600-139794800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:139793600-139794800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:139793600-139794800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr6:139793600-139794800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:139793600-139794800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr6:139793600-139794800	Enhancers	Right Atrium	heart
17	chr6:139793600-139795200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:139793600-139795200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:139793600-139795200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:139793600-139795200	Enhancers	Fetal Muscle Leg	muscle
21	chr6:139793600-139795200	Enhancers	K562	blood
22	chr6:139793600-139795200	Enhancers	Osteobl	bone
23	chr6:139793600-139795400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:139793600-139795400	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr6:139793600-139795400	Enhancers	Brain Anterior Caudate	brain
26	chr6:139793600-139795400	Enhancers	Colon Smooth Muscle	Colon
27	chr6:139793600-139795400	Enhancers	Fetal Lung	lung
28	chr6:139793600-139795400	Enhancers	HSMMtube	muscle
29	chr6:139793600-139795400	Enhancers	NHLF	lung
30	chr6:139793600-139796200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:139793600-139796200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:139793600-139796800	Enhancers	H9 Cell Line	embryonic stem cell
33	chr6:139793600-139796800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:139793600-139797200	Enhancers	Fetal Stomach	stomach
35	chr6:139793600-139797600	Enhancers	Fetal Brain Male	brain
36	chr6:139793800-139795200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:139793800-139795200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr6:139793800-139795400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:139793800-139795400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:139793800-139795400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:139793800-139795400	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:139793800-139795400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:139793800-139795600	Enhancers	Esophagus	oesophagus
44	chr6:139793800-139796200	Enhancers	Placenta	Placenta
45	chr6:139794000-139794400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:139794000-139794600	Enhancers	Brain Angular Gyrus	brain
47	chr6:139794000-139794600	Enhancers	Ovary	ovary
48	chr6:139794000-139794800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:139794000-139794800	Flanking Active TSS	Liver	Liver
50	chr6:139794000-139794800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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