Variant report

Variant	rs12134601
Chromosome Location	chr1:181012229-181012230
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180990073..180993369-chr1:181008815..181014232,9	MCF-7	breast:
2	chr1:181004788..181008643-chr1:181010792..181015908,7	K562	blood:
3	chr1:181010770..181016050-chr1:181055138..181060794,9	MCF-7	breast:
4	chr1:181001684..181003948-chr1:181009601..181013491,4	K562	blood:
5	chr1:181011084..181016329-chr1:181056547..181060434,6	K562	blood:
6	chr1:180999745..181016101-chr1:181055432..181063450,33	K562	blood:
7	chr1:181004593..181007804-chr1:181008315..181013552,8	K562	blood:
8	chr1:181003253..181008679-chr1:181011469..181014538,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000153029	Chromatin interaction
ENSG00000135823	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10157092	0.95[JPT][hapmap]
rs10159067	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10159443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10218681	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16856661	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856663	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34260849	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806284	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3845422	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3892173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55764324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55903939	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56030303	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56089565	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658363	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535177	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1011081	chr1:180973159-181135953	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12134601	STX6	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:181004000-181013600	Weak transcription	Psoas Muscle	Psoas
2	chr1:181004000-181015600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:181004000-181025400	Weak transcription	Fetal Stomach	stomach
4	chr1:181004000-181025800	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:181004000-181026200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:181005600-181013800	Weak transcription	Pancreas	Pancrea
7	chr1:181005600-181025800	Weak transcription	Right Ventricle	heart
8	chr1:181005600-181026000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:181005600-181026400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:181005600-181028200	Weak transcription	Gastric	stomach
11	chr1:181005600-181028600	Weak transcription	Ovary	ovary
12	chr1:181007200-181026600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:181008600-181020800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:181008600-181031400	Weak transcription	NHLF	lung
15	chr1:181008800-181022800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:181009600-181014600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:181009800-181013400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:181009800-181013600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:181010200-181013800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:181010600-181012400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:181010600-181014200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr1:181010800-181013400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:181010800-181013400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:181010800-181024600	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:181011000-181018400	Weak transcription	HSMM	muscle
26	chr1:181011000-181025600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:181011000-181031400	Weak transcription	Osteobl	bone
28	chr1:181011200-181019200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:181011200-181024600	Weak transcription	Aorta	Aorta
30	chr1:181011800-181012400	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:181011800-181012600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:181011800-181013000	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr1:181011800-181013000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:181011800-181013000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:181011800-181013400	Enhancers	HepG2	liver
36	chr1:181011800-181013400	Enhancers	NHEK	skin
37	chr1:181011800-181013800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:181011800-181013800	Enhancers	Fetal Intestine Large	intestine
39	chr1:181011800-181013800	Enhancers	Fetal Intestine Small	intestine
40	chr1:181011800-181013800	Enhancers	A549	lung
41	chr1:181011800-181014000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr1:181011800-181014200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:181011800-181014200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr1:181011800-181014200	Enhancers	Duodenum Mucosa	Duodenum
45	chr1:181011800-181014400	Enhancers	Liver	Liver
46	chr1:181011800-181015000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr1:181012000-181012400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:181012000-181012400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:181012000-181012600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:181012000-181012600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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