Variant report

Variant	rs1410599
Chromosome Location	chr10:97070709-97070710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97049242..97050860-chr10:97068797..97070801,3	MCF-7	breast:
2	chr10:97063353..97065156-chr10:97068953..97071321,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107438	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10509694	0.88[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10882589	0.81[CHB][hapmap]
rs11188273	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11188277	1.00[JPT][hapmap]
rs11188283	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs11188284	0.94[JPT][hapmap]
rs11188301	0.81[CHB][hapmap]
rs11188312	0.81[CHB][hapmap]
rs12217735	0.81[CHB][hapmap]
rs1410058	0.81[CHB][hapmap]
rs1410605	1.00[CEU][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap]
rs1556054	0.81[JPT][hapmap]
rs17110604	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17110702	0.81[CHB][hapmap]
rs36112739	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3740509	0.81[CHB][hapmap]
rs41528346	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs4918927	0.81[CHB][hapmap]
rs67035837	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs726175	0.84[JPT][hapmap]
rs874450	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv552021	chr10:97053404-97071334	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1410599	ANKRD2	cis	parietal	SCAN
rs1410599	PDLIM1	cis	cerebellum	SCAN
rs1410599	FRAT2	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97055600-97072800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr10:97063400-97072400	Weak transcription	Fetal Brain Female	brain
3	chr10:97063400-97073600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:97064000-97073200	Weak transcription	Fetal Muscle Leg	muscle
5	chr10:97064600-97078200	Weak transcription	Colonic Mucosa	Colon
6	chr10:97066000-97073000	Weak transcription	Fetal Intestine Large	intestine
7	chr10:97066000-97073600	Weak transcription	Fetal Intestine Small	intestine
8	chr10:97067000-97070800	Enhancers	Stomach Mucosa	stomach
9	chr10:97067200-97073400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr10:97067600-97070800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr10:97067600-97071200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:97067800-97071000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr10:97068200-97071000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr10:97068400-97071000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr10:97068400-97072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr10:97068600-97071000	Enhancers	Primary B cells from peripheral blood	blood
17	chr10:97068600-97072000	Weak transcription	Adipose Nuclei	Adipose
18	chr10:97068600-97072800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:97068600-97073800	Weak transcription	Brain Angular Gyrus	brain
20	chr10:97069000-97070800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr10:97069000-97072400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:97069000-97073000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:97069000-97073200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr10:97069000-97073400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr10:97069000-97073600	Weak transcription	HepG2	liver
26	chr10:97069000-97075600	Enhancers	K562	blood
27	chr10:97069200-97072200	Weak transcription	HUVEC	blood vessel
28	chr10:97069200-97072600	Weak transcription	Psoas Muscle	Psoas
29	chr10:97069200-97072600	Weak transcription	HSMMtube	muscle
30	chr10:97069200-97087000	Weak transcription	HSMM	muscle
31	chr10:97069400-97072400	Weak transcription	Left Ventricle	heart
32	chr10:97069400-97072600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:97069400-97074000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:97069600-97072000	Weak transcription	Hela-S3	cervix
35	chr10:97069600-97073000	Weak transcription	Fetal Stomach	stomach
36	chr10:97069600-97073800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:97069800-97070800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr10:97069800-97071000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:97069800-97072200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:97069800-97075200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:97070000-97071000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr10:97070000-97071000	Enhancers	Gastric	stomach
43	chr10:97070000-97071200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr10:97070000-97073000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:97070200-97070800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr10:97070200-97070800	Enhancers	Small Intestine	intestine
47	chr10:97070200-97071000	Genic enhancers	Aorta	Aorta
48	chr10:97070200-97071000	Enhancers	Esophagus	oesophagus
49	chr10:97070200-97071000	Enhancers	Spleen	Spleen
50	chr10:97070200-97071200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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