Variant report

Variant	rs789743
Chromosome Location	chr12:64481843-64481844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64236335..64238205-chr12:64481368..64483415,2	MCF-7	breast:
2	chr12:64481819..64484735-chr12:64488926..64491185,2	MCF-7	breast:
3	chr12:64479951..64485061-chr12:64487402..64490440,5	MCF-7	breast:
4	chr12:64473507..64478199-chr12:64480317..64485815,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1456042	0.81[EUR][1000 genomes]
rs1565942	0.82[EUR][1000 genomes]
rs1827074	0.83[EUR][1000 genomes]
rs57477949	0.85[EUR][1000 genomes]
rs789709	0.92[CEU][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs789743	SRGAP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64457000-64510600	Weak transcription	HepG2	liver
2	chr12:64467000-64482400	Weak transcription	Aorta	Aorta
3	chr12:64471000-64482400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:64472200-64482000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:64473800-64482000	Weak transcription	Fetal Intestine Large	intestine
6	chr12:64474400-64482400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:64474600-64482400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:64474600-64482600	Weak transcription	Left Ventricle	heart
9	chr12:64474800-64521400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:64475000-64482000	Weak transcription	Fetal Intestine Small	intestine
11	chr12:64475200-64482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:64475200-64482400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:64475200-64482400	Weak transcription	Right Ventricle	heart
14	chr12:64475400-64486000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:64476800-64482800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:64476800-64482800	Weak transcription	Spleen	Spleen
17	chr12:64477000-64482400	Weak transcription	Placenta	Placenta
18	chr12:64477000-64482400	Weak transcription	Pancreas	Pancrea
19	chr12:64477000-64482800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:64477000-64482800	Weak transcription	Lung	lung
21	chr12:64477000-64482800	Weak transcription	Right Atrium	heart
22	chr12:64477200-64482400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:64477200-64482400	Weak transcription	Liver	Liver
24	chr12:64477200-64482800	Weak transcription	Psoas Muscle	Psoas
25	chr12:64477400-64520800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:64477600-64482200	Weak transcription	Fetal Kidney	kidney
27	chr12:64477600-64482400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:64477800-64482000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:64477800-64482000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:64477800-64482200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:64477800-64482400	Weak transcription	Brain Angular Gyrus	brain
32	chr12:64477800-64482600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:64478000-64482200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:64478000-64482400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:64478000-64483400	Weak transcription	Brain Substantia Nigra	brain
36	chr12:64478200-64482000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:64478200-64482200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:64478400-64482600	Weak transcription	Brain Germinal Matrix	brain
39	chr12:64479400-64482000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:64479400-64482400	Enhancers	NHLF	lung
41	chr12:64479400-64482800	Enhancers	NHDF-Ad	bronchial
42	chr12:64479600-64482000	Weak transcription	Fetal Brain Male	brain
43	chr12:64479800-64483000	Enhancers	Rectal Smooth Muscle	rectum
44	chr12:64480000-64482200	Weak transcription	Fetal Muscle Leg	muscle
45	chr12:64480000-64482400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr12:64480000-64482400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:64480000-64482400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:64480000-64482800	Weak transcription	Esophagus	oesophagus
49	chr12:64480200-64482000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:64480200-64482000	Enhancers	A549	lung

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