Variant report

Variant	rs3846880
Chromosome Location	chr6:37633106-37633107
allele	A/T
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	KAP1	chr6:37633014-37633664	U2OS	brain:	n/a	n/a
2	KAP1	chr6:37633049-37633663	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
MDGA1	TF binding region

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs6903131	0.81[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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3846880	TCP11	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37626000-37633400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:37626000-37635000	Weak transcription	A549	lung
3	chr6:37629200-37635000	Weak transcription	Aorta	Aorta
4	chr6:37629400-37646000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:37629600-37641000	Weak transcription	Fetal Brain Female	brain
6	chr6:37629600-37659600	Weak transcription	Ovary	ovary
7	chr6:37630400-37634600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:37630600-37633600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:37630600-37633800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:37630800-37633600	Enhancers	Brain Angular Gyrus	brain
11	chr6:37630800-37633600	Enhancers	Brain Hippocampus Middle	brain
12	chr6:37630800-37633800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:37631000-37633600	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:37631000-37633600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:37631200-37633400	Enhancers	Brain Anterior Caudate	brain
16	chr6:37631600-37633600	Enhancers	Gastric	stomach
17	chr6:37631600-37635000	Weak transcription	Osteobl	bone
18	chr6:37631800-37633600	Enhancers	Fetal Muscle Leg	muscle
19	chr6:37631800-37634600	Weak transcription	NHLF	lung
20	chr6:37631800-37634800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:37631800-37635000	Weak transcription	NH-A	brain
22	chr6:37631800-37635000	Weak transcription	NHDF-Ad	bronchial
23	chr6:37631800-37647600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr6:37632000-37633200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:37632000-37633600	Enhancers	Brain Substantia Nigra	brain
26	chr6:37632000-37634800	Weak transcription	Fetal Brain Male	brain
27	chr6:37632200-37633600	Enhancers	Right Atrium	heart
28	chr6:37632200-37633800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:37632400-37633800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:37632600-37633600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:37632600-37633600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:37632600-37634800	Weak transcription	HSMMtube	muscle
33	chr6:37632800-37633200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:37632800-37633400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:37632800-37633400	Enhancers	Left Ventricle	heart
36	chr6:37632800-37633600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:37632800-37633600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr6:37632800-37633600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:37632800-37633600	Enhancers	Placenta	Placenta
40	chr6:37632800-37633600	Enhancers	K562	blood
41	chr6:37632800-37633800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:37632800-37633800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:37632800-37633800	Enhancers	Fetal Heart	heart
44	chr6:37633000-37633200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:37633000-37633200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:37633000-37633400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:37633000-37633400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:37633000-37633600	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:37633000-37633600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr6:37633000-37633600	Enhancers	Right Ventricle	heart

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