Variant report

Variant	rs12240946
Chromosome Location	chr10:98756813-98756814
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98754213..98757078-chr10:98760564..98763422,2	MCF-7	breast:
2	chr10:98755934..98759369-chr10:98763057..98767481,4	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10437452	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188929	1.00[ASN][1000 genomes]
rs11188937	1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[YRI][hapmap]
rs11188939	0.85[GIH][hapmap]
rs11188956	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap]
rs11188959	1.00[GIH][hapmap];0.88[MEX][hapmap]
rs11188967	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs11188971	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs11188978	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188999	1.00[ASN][1000 genomes]
rs12241405	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241564	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242330	1.00[GIH][hapmap];0.88[MEX][hapmap]
rs12243551	1.00[GIH][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs12244490	1.00[ASN][1000 genomes]
rs12246067	0.91[YRI][hapmap]
rs12248349	1.00[ASN][1000 genomes]
rs12249381	1.00[GIH][hapmap];0.88[MEX][hapmap];0.87[YRI][hapmap]
rs12250548	1.00[ASN][1000 genomes]
rs12252424	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs12254525	1.00[ASN][1000 genomes]
rs12262784	1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap]
rs12264014	1.00[ASN][1000 genomes]
rs12264950	1.00[ASN][1000 genomes]
rs12265242	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[YRI][hapmap]
rs12265606	1.00[ASN][1000 genomes]
rs12267926	0.91[YRI][hapmap]
rs12268216	0.85[GIH][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap]
rs12268272	1.00[CEU][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap]
rs17112175	1.00[GIH][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap]
rs17112190	1.00[GIH][hapmap];0.88[MEX][hapmap]
rs2183449	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505353	1.00[ASN][1000 genomes]
rs4394767	0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs55855950	1.00[ASN][1000 genomes]
rs56327223	1.00[ASN][1000 genomes]
rs57501540	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270704	1.00[ASN][1000 genomes]
rs58409956	1.00[ASN][1000 genomes]
rs6584101	1.00[ASN][1000 genomes]
rs7071211	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072273	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap]
rs7073150	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081197	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082838	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085822	1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap]
rs7086875	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090441	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090690	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090880	1.00[ASN][1000 genomes]
rs72821721	1.00[ASN][1000 genomes]
rs72821744	1.00[ASN][1000 genomes]
rs72821759	1.00[ASN][1000 genomes]
rs73318637	1.00[ASN][1000 genomes]
rs73318641	1.00[ASN][1000 genomes]
rs73320607	1.00[ASN][1000 genomes]
rs74153734	1.00[ASN][1000 genomes]
rs7893325	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894138	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895914	1.00[ASN][1000 genomes]
rs7906294	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910221	0.88[MEX][hapmap]
rs7918085	1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[YRI][hapmap]
rs7920238	1.00[CEU][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921885	1.00[GIH][hapmap]

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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831951	chr10:98717103-98761280	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12240946	CCNJ	cis	cerebellum	SCAN
rs12240946	CRTAC1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98741200-98758000	Weak transcription	K562	blood
2	chr10:98742000-98757000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr10:98743000-98758600	Weak transcription	Spleen	Spleen
4	chr10:98743800-98758000	Weak transcription	Fetal Brain Female	brain
5	chr10:98745000-98758400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:98745200-98760400	Weak transcription	Primary T cells from cord blood	blood
7	chr10:98745400-98757600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:98746400-98758600	Weak transcription	Esophagus	oesophagus
9	chr10:98748200-98758200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:98748800-98757600	Weak transcription	Brain Germinal Matrix	brain
11	chr10:98751600-98758200	Weak transcription	Placenta	Placenta
12	chr10:98751600-98760200	Weak transcription	A549	lung
13	chr10:98753000-98757400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr10:98753000-98759800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr10:98753000-98760000	Weak transcription	Gastric	stomach
16	chr10:98753000-98762400	Weak transcription	Thymus	Thymus
17	chr10:98753000-98765200	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:98753200-98757200	Weak transcription	Fetal Thymus	thymus
19	chr10:98754000-98757000	Enhancers	Fetal Heart	heart
20	chr10:98755000-98757600	Weak transcription	Right Ventricle	heart
21	chr10:98755200-98757600	Weak transcription	Fetal Intestine Large	intestine
22	chr10:98755400-98757000	Enhancers	HSMMtube	muscle
23	chr10:98755600-98757000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:98755600-98759600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr10:98755800-98757600	Weak transcription	Fetal Intestine Small	intestine
26	chr10:98756000-98758000	Weak transcription	Fetal Lung	lung
27	chr10:98756000-98758200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:98756200-98757400	Weak transcription	HepG2	liver
29	chr10:98756200-98758200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:98756200-98758200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr10:98756200-98780000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:98756400-98758400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr10:98756400-98758400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr10:98756400-98764600	Weak transcription	Brain Angular Gyrus	brain
35	chr10:98756600-98757000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr10:98756600-98758000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr10:98756600-98758200	Weak transcription	Osteobl	bone
38	chr10:98756600-98758400	Weak transcription	Ovary	ovary
39	chr10:98756600-98758600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr10:98756600-98760400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr10:98756800-98757400	Enhancers	Lung	lung
42	chr10:98756800-98758000	Weak transcription	NH-A	brain

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