Variant report

Variant	rs12894596
Chromosome Location	chr14:81733964-81733965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:81684377..81689943-chr14:81728055..81734631,10	K562	blood:
2	chr14:81727889..81730386-chr14:81731826..81734332,3	MCF-7	breast:
3	chr14:81732900..81735880-chr14:81918109..81921076,5	MCF-7	breast:
4	chr14:81733496..81737456-chr14:81918664..81922273,4	MCF-7	breast:
5	chr14:81684348..81690583-chr14:81729061..81738251,32	MCF-7	breast:
6	chr14:81683224..81690294-chr14:81730621..81737433,21	MCF-7	breast:
7	chr14:81684594..81689943-chr14:81730721..81738333,8	K562	blood:
8	chr14:81733159..81735915-chr14:81931086..81932603,2	K562	blood:
9	chr14:81733049..81735838-chr14:81736167..81738052,2	MCF-7	breast:
10	chr14:81728442..81730131-chr14:81732083..81734711,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000165417	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10131728	1.00[CHB][hapmap]
rs12878339	1.00[CHB][hapmap]
rs12878503	1.00[CHB][hapmap]
rs12880551	1.00[CHB][hapmap]
rs12889291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12891828	1.00[CHB][hapmap]
rs12892815	1.00[CHB][hapmap]
rs12895215	1.00[CHB][hapmap]
rs17111613	1.00[JPT][hapmap]
rs17111624	1.00[JPT][hapmap]
rs17111629	1.00[JPT][hapmap]
rs17630746	1.00[CHB][hapmap]
rs7148747	1.00[JPT][hapmap]
rs7149917	1.00[JPT][hapmap]
rs7153668	1.00[JPT][hapmap]

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	nsv832841	chr14:81588322-81743921	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12894596	NRXN3	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:81714200-81738600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:81714400-81734000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr14:81719800-81735600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr14:81721200-81735600	Weak transcription	Brain Anterior Caudate	brain
5	chr14:81721200-81742400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr14:81721400-81739800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:81721600-81739800	Weak transcription	Ovary	ovary
8	chr14:81722600-81741800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr14:81723000-81734200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr14:81723400-81734000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr14:81723400-81734200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:81724400-81735400	Weak transcription	Fetal Intestine Large	intestine
13	chr14:81724600-81736400	Weak transcription	Fetal Intestine Small	intestine
14	chr14:81724600-81741800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr14:81724600-81746000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:81724800-81736400	Weak transcription	Spleen	Spleen
17	chr14:81725000-81739800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr14:81725000-81740000	Weak transcription	Esophagus	oesophagus
19	chr14:81725000-81743600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr14:81725600-81734000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr14:81725600-81734400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:81725800-81734200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr14:81725800-81734200	Strong transcription	NHEK	skin
24	chr14:81726400-81734200	Weak transcription	Placenta	Placenta
25	chr14:81726800-81736600	Weak transcription	Brain Substantia Nigra	brain
26	chr14:81727600-81736800	Weak transcription	Psoas Muscle	Psoas
27	chr14:81727800-81734200	Weak transcription	Fetal Muscle Leg	muscle
28	chr14:81727800-81746200	Weak transcription	NHDF-Ad	bronchial
29	chr14:81728000-81736600	Weak transcription	Fetal Brain Male	brain
30	chr14:81728200-81734200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:81729000-81735800	Weak transcription	Brain Hippocampus Middle	brain
32	chr14:81729400-81752600	Weak transcription	Stomach Mucosa	stomach
33	chr14:81730600-81734000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr14:81730600-81734200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr14:81730600-81734200	Weak transcription	HMEC	breast
36	chr14:81730600-81743000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr14:81730600-81744000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr14:81730800-81735600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr14:81730800-81740000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr14:81730800-81743600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr14:81731200-81734000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr14:81731600-81739200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr14:81732000-81734200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr14:81732000-81735800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:81732200-81734000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr14:81732400-81743600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr14:81732600-81735600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr14:81733000-81734000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr14:81733000-81734000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr14:81733000-81734000	Weak transcription	Fetal Thymus	thymus

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