Variant report

Variant	rs12198214
Chromosome Location	chr6:69346439-69346440
allele	G/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	RAD21	chr6:69342384-69347457	SK-N-SH	brain:	n/a	chr6:69345907-69345917 chr6:69345020-69345034 chr6:69344689-69344699 chr6:69343839-69343849 chr6:69345328-69345338
2	RAD21	chr6:69346042-69346453	H1-hESC	embryonic stem cell:	n/a	n/a
3	RFX5	chr6:69342558-69347581	SK-N-SH	brain:	n/a	chr6:69344290-69344305 chr6:69346927-69346936 chr6:69344290-69344305
4	RFX5	chr6:69345606-69346451	K562	blood:	n/a	n/a
5	ZNF384	chr6:69346390-69346974	K562	blood:	n/a	n/a
6	RAD21	chr6:69345780-69346451	SK-N-SH_RA	brain:	n/a	chr6:69345907-69345917
7	ZC3H11A	chr6:69346216-69346501	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000230910	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10945133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10945134	1.00[ASW][hapmap]
rs12211047	1.00[CHB][hapmap]
rs12216491	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17198341	1.00[CHB][hapmap]
rs2802704	0.81[EUR][1000 genomes]
rs2802705	0.84[CEU][hapmap]
rs4554295	0.84[CEU][hapmap]
rs7743914	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7754547	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9346237	1.00[ASW][hapmap]

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	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830680	chr6:69192214-69351103	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12198214	SMAP1	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69342600-69349600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:69342600-69351000	Active TSS	Brain Angular Gyrus	brain
3	chr6:69342800-69348000	Active TSS	Fetal Brain Male	brain
4	chr6:69343000-69348000	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr6:69343200-69348600	Active TSS	Brain Cingulate Gyrus	brain
6	chr6:69343200-69348800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:69343200-69349200	Active TSS	Brain Germinal Matrix	brain
8	chr6:69343200-69351200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:69343200-69352000	Active TSS	Brain Anterior Caudate	brain
10	chr6:69343400-69348400	Active TSS	Fetal Stomach	stomach
11	chr6:69343400-69349600	Active TSS	Fetal Brain Female	brain
12	chr6:69343600-69346600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:69343600-69346800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:69343600-69347200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr6:69343600-69347400	Active TSS	Brain Substantia Nigra	brain
16	chr6:69343600-69348200	Active TSS	Right Atrium	heart
17	chr6:69343800-69346600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:69343800-69346600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:69343800-69346600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:69343800-69346600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:69343800-69346600	Active TSS	Left Ventricle	heart
22	chr6:69343800-69346800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr6:69343800-69346800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:69343800-69346800	Active TSS	Ovary	ovary
25	chr6:69343800-69347400	Active TSS	Colon Smooth Muscle	Colon
26	chr6:69344000-69346600	Active TSS	Aorta	Aorta
27	chr6:69344000-69346800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr6:69344000-69347000	Active TSS	Right Ventricle	heart
29	chr6:69344200-69346600	Bivalent/Poised TSS	NH-A	brain
30	chr6:69344200-69346800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:69344200-69347000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:69344200-69347000	Active TSS	Brain Hippocampus Middle	brain
33	chr6:69344200-69347000	Active TSS	K562	blood
34	chr6:69344200-69347200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr6:69344400-69347000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr6:69344400-69347000	Active TSS	Fetal Lung	lung
37	chr6:69345200-69346800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:69345400-69346600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr6:69345600-69346600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr6:69345600-69346600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:69345600-69346600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:69345800-69346800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:69345800-69346800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
44	chr6:69345800-69346800	Bivalent/Poised TSS	Fetal Kidney	kidney
45	chr6:69346000-69346600	Active TSS	Adipose Nuclei	Adipose
46	chr6:69346000-69346600	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
47	chr6:69346200-69346600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:69346200-69346600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
49	chr6:69346200-69346600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:69346200-69346600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin

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