Variant report

Variant	rs3816896
Chromosome Location	chr12:58195773-58195774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58195728-58195924	HepG2	liver:	n/a	n/a
2	E2F4	chr12:58195651-58195811	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58195714..58198546-chr12:58205658..58208467,2	K562	blood:
2	chr12:58194367..58196238-chr12:58334648..58336913,2	MCF-7	breast:
3	chr12:58193274..58197647-chr12:58200040..58205215,7	MCF-7	breast:
4	chr12:58193083..58195833-chr12:58196362..58200712,4	K562	blood:
5	chr12:57912401..57915240-chr12:58195290..58197109,2	MCF-7	breast:
6	chr12:58194136..58195833-chr12:58195975..58197862,2	K562	blood:

No data

Variant related genes	Relation type
AVIL	TF binding region
ENSG00000270039	TF binding region
ENSG00000166987	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000269903	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000206749	Chromatin interaction
ENSG00000270039	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10877020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172337	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12368653	0.81[EUR][1000 genomes]
rs2277326	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2307097	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[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	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3816896	XRCC6BP1	cis	Artery Tibial	GTEx
rs3816896	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs3816896	NR3C1	trans	lymphoblastoid	RTeQTL
rs3816896	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs3816896	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs3816896	XRCC6BP1	cis	Whole Blood	GTEx
rs3816896	FAM119B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart
3	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:58177800-58198400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr12:58177800-58198400	Strong transcription	Fetal Muscle Leg	muscle
6	chr12:58177800-58199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:58178000-58197200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr12:58178000-58197600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:58178000-58198200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:58178000-58198200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:58178000-58198200	Strong transcription	Fetal Thymus	thymus
12	chr12:58178200-58197000	Strong transcription	Fetal Intestine Large	intestine
13	chr12:58178200-58197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:58178200-58198200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:58178600-58207600	Strong transcription	Liver	Liver
16	chr12:58179000-58196800	Strong transcription	Thymus	Thymus
17	chr12:58179000-58197600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:58179000-58198200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:58179200-58199000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:58179400-58197400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr12:58181400-58216000	Weak transcription	Fetal Brain Male	brain
22	chr12:58183000-58198200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr12:58185400-58197000	Strong transcription	Fetal Brain Female	brain
24	chr12:58185600-58198800	Strong transcription	Primary T cells from cord blood	blood
25	chr12:58185800-58197000	Strong transcription	Brain Germinal Matrix	brain
26	chr12:58186200-58196800	Strong transcription	Brain Hippocampus Middle	brain
27	chr12:58186600-58198200	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:58187000-58216600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:58187200-58215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:58187400-58197200	Strong transcription	Brain Anterior Caudate	brain
31	chr12:58188400-58197200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:58188600-58207800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:58189000-58197200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr12:58189000-58208400	Strong transcription	Fetal Stomach	stomach
35	chr12:58189200-58207800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:58189400-58197200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:58189400-58197200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:58189400-58197200	Strong transcription	Osteobl	bone
39	chr12:58189400-58197400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr12:58189400-58198200	Strong transcription	NHLF	lung
41	chr12:58189400-58207200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:58189600-58197200	Strong transcription	Colon Smooth Muscle	Colon
43	chr12:58189600-58197400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:58189600-58197600	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:58189600-58200200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:58189800-58197000	Strong transcription	Left Ventricle	heart
47	chr12:58189800-58197200	Strong transcription	HSMMtube	muscle
48	chr12:58189800-58198400	Strong transcription	NHDF-Ad	bronchial
49	chr12:58189800-58208400	Strong transcription	Placenta	Placenta
50	chr12:58190200-58216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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