Variant report

Variant	rs17537670
Chromosome Location	chr2:208834260-208834261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10497895	0.81[GIH][hapmap]
rs12464255	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs12465292	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12471242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13431014	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1452521	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17459574	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17459758	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17538061	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs28463196	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4502388	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62190863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62190896	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62190898	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62190900	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62190904	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62190905	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6435402	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6740362	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72969822	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7565251	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7588162	0.87[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs930745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17537670	CREB1	cis	parietal	SCAN
rs17537670	SNORA41	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208796000-208835200	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:208810400-208841000	Weak transcription	Fetal Lung	lung
3	chr2:208811200-208835200	Weak transcription	Brain Angular Gyrus	brain
4	chr2:208815400-208835400	Weak transcription	Right Ventricle	heart
5	chr2:208815400-208840800	Weak transcription	Ovary	ovary
6	chr2:208817200-208834600	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:208825200-208841400	Weak transcription	Aorta	Aorta
8	chr2:208825600-208841400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:208826600-208841400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:208826800-208840800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:208827200-208841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:208827200-208841400	Weak transcription	Pancreas	Pancrea
13	chr2:208827400-208834800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:208827400-208835200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:208827400-208841400	Weak transcription	Left Ventricle	heart
16	chr2:208827400-208841400	Weak transcription	Lung	lung
17	chr2:208827400-208857400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:208827600-208834800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:208827800-208840800	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:208828000-208834400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:208828000-208834800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:208828000-208834800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:208828000-208840800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:208828000-208841000	Weak transcription	Fetal Thymus	thymus
25	chr2:208828200-208834600	Weak transcription	Primary B cells from cord blood	blood
26	chr2:208828200-208835000	Weak transcription	Primary T cells from cord blood	blood
27	chr2:208828200-208838600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr2:208828200-208838600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr2:208828200-208840400	Weak transcription	Thymus	Thymus
30	chr2:208828200-208841400	Weak transcription	Dnd41	blood
31	chr2:208831000-208834400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:208831800-208834400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:208831800-208836000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:208832000-208836800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:208832200-208834600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:208832200-208834600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr2:208832400-208834600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:208832600-208834600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
39	chr2:208832600-208835200	Weak transcription	Fetal Brain Female	brain
40	chr2:208832600-208835800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:208832600-208836200	Enhancers	Duodenum Mucosa	Duodenum
42	chr2:208832800-208834400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:208832800-208836200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:208832800-208841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:208833200-208835600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr2:208833400-208834800	Weak transcription	Psoas Muscle	Psoas
47	chr2:208833400-208835200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:208833400-208836800	Enhancers	Fetal Intestine Small	intestine
49	chr2:208833600-208835800	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr2:208834000-208834600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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