Variant report

Variant	rs6738748
Chromosome Location	chr2:39924741-39924742
allele	C/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	RAD21	chr2:39923183-39924750	SK-N-SH	brain:	n/a	chr2:39924087-39924106

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39740456..39741440-chr2:39923994..39925288,5	MCF-7	breast:

Variant related genes	Relation type
TMEM178A	TF binding region
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10193803	1.00[JPT][hapmap]
rs13423235	1.00[JPT][hapmap]
rs17024197	1.00[ASN][1000 genomes]
rs17024202	1.00[ASN][1000 genomes]
rs17024218	1.00[ASN][1000 genomes]
rs17024232	1.00[ASN][1000 genomes]
rs2540243	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2540245	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2716698	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2716700	1.00[ASN][1000 genomes]
rs2716702	1.00[ASN][1000 genomes]
rs2716709	1.00[ASN][1000 genomes]
rs2716733	1.00[ASN][1000 genomes]
rs56104365	1.00[ASN][1000 genomes]
rs58054718	1.00[ASN][1000 genomes]
rs72934285	1.00[ASN][1000 genomes]
rs72934295	1.00[ASN][1000 genomes]
rs72936030	1.00[ASN][1000 genomes]
rs72936034	1.00[ASN][1000 genomes]
rs72936037	1.00[ASN][1000 genomes]
rs72936041	1.00[ASN][1000 genomes]
rs72936044	1.00[ASN][1000 genomes]
rs72936047	1.00[ASN][1000 genomes]
rs72936048	1.00[ASN][1000 genomes]
rs72936053	1.00[ASN][1000 genomes]
rs72936058	1.00[ASN][1000 genomes]
rs73924940	1.00[ASN][1000 genomes]
rs73927043	1.00[ASN][1000 genomes]
rs990405	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39914200-39926800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:39921400-39924800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39921600-39925200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:39921600-39925200	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:39922000-39924800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:39922000-39925200	Enhancers	HSMMtube	muscle
7	chr2:39922200-39925000	Enhancers	Fetal Stomach	stomach
8	chr2:39922200-39925200	Enhancers	Fetal Lung	lung
9	chr2:39922400-39925200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:39922400-39925200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:39922600-39925000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:39922600-39925200	Enhancers	Brain Angular Gyrus	brain
13	chr2:39922800-39925200	Enhancers	Psoas Muscle	Psoas
14	chr2:39923000-39925200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:39923200-39924800	Enhancers	HUVEC	blood vessel
16	chr2:39923200-39925000	Enhancers	Brain Substantia Nigra	brain
17	chr2:39923200-39925200	Enhancers	Brain Anterior Caudate	brain
18	chr2:39923200-39925200	Enhancers	Colon Smooth Muscle	Colon
19	chr2:39923200-39925600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:39923400-39924800	Enhancers	Adipose Nuclei	Adipose
21	chr2:39923400-39924800	Enhancers	Osteobl	bone
22	chr2:39923400-39925000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:39923400-39925000	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:39923400-39925200	Enhancers	Fetal Brain Male	brain
25	chr2:39923400-39925400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:39923400-39925600	Enhancers	Fetal Brain Female	brain
27	chr2:39923600-39926200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:39923600-39935200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:39923800-39924800	Weak transcription	Left Ventricle	heart
30	chr2:39923800-39925200	Enhancers	HMEC	breast
31	chr2:39923800-39925200	Enhancers	HSMM	muscle
32	chr2:39924000-39925000	Weak transcription	NH-A	brain
33	chr2:39924200-39924800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:39924200-39926000	Enhancers	Fetal Heart	heart
35	chr2:39924400-39925200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:39924400-39925200	Enhancers	Fetal Muscle Leg	muscle
37	chr2:39924600-39925200	Enhancers	H9 Cell Line	embryonic stem cell
38	chr2:39924600-39925200	Enhancers	Brain Hippocampus Middle	brain
39	chr2:39924600-39925200	Enhancers	Right Atrium	heart

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