Variant report

Variant	rs7893325
Chromosome Location	chr10:98755080-98755081
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	chr10:98754213..98757078-chr10:98760564..98763422,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C10orf12-1	chr10:98752207-98755716	ENSG00000231025.1
2	lnc-C10orf12-1	chr10:98753748-98755713	NONHSAT015844

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10437452	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188929	1.00[ASN][1000 genomes]
rs11188937	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs11188939	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap]
rs11188954	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11188955	0.86[EUR][1000 genomes]
rs11188956	0.87[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11188959	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11188967	0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs11188971	0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11188978	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188999	1.00[ASN][1000 genomes]
rs12240946	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241405	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241564	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242330	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs12243551	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs12244490	1.00[ASN][1000 genomes]
rs12246067	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs12247344	0.82[EUR][1000 genomes]
rs12248349	1.00[ASN][1000 genomes]
rs12249381	0.87[ASW][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12249427	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12250548	1.00[ASN][1000 genomes]
rs12252424	0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs12252435	1.00[CEU][hapmap]
rs12254525	1.00[ASN][1000 genomes]
rs12257413	0.86[EUR][1000 genomes]
rs12258355	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12258469	0.86[EUR][1000 genomes]
rs12262784	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs12263331	0.86[EUR][1000 genomes]
rs12264014	1.00[ASN][1000 genomes]
rs12264950	1.00[ASN][1000 genomes]
rs12265242	0.93[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs12265606	1.00[ASN][1000 genomes]
rs12267926	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs12268216	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs12268272	0.93[ASW][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs13376965	0.86[EUR][1000 genomes]
rs17112175	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs17112190	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2183449	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28439735	0.86[EUR][1000 genomes]
rs28505353	1.00[ASN][1000 genomes]
rs28758432	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4394767	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55855950	1.00[ASN][1000 genomes]
rs56327223	1.00[ASN][1000 genomes]
rs56867696	0.86[EUR][1000 genomes]
rs57501540	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270704	1.00[ASN][1000 genomes]
rs58376960	0.84[EUR][1000 genomes]
rs58409956	1.00[ASN][1000 genomes]
rs59938221	0.82[EUR][1000 genomes]
rs59999388	0.86[EUR][1000 genomes]
rs60576681	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61492214	0.86[EUR][1000 genomes]
rs6584101	1.00[ASN][1000 genomes]
rs7071211	0.93[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072273	0.87[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7073150	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081197	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7082316	0.86[EUR][1000 genomes]
rs7082838	0.87[ASW][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085822	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes]
rs7085851	0.86[EUR][1000 genomes]
rs7086875	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090441	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7090690	0.96[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]
rs7894138	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895914	1.00[ASN][1000 genomes]
rs7906294	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910221	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs7918085	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs7920238	0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921885	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7893325	ENTPD7	cis	cerebellum	SCAN
rs7893325	CCNJ	cis	cerebellum	SCAN
rs7893325	CWF19L1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

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	chr10:98742600-98755800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:98742600-98756000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:98742600-98756800	Weak transcription	Lung	lung
6	chr10:98743000-98758600	Weak transcription	Spleen	Spleen
7	chr10:98743800-98758000	Weak transcription	Fetal Brain Female	brain
8	chr10:98745000-98758400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:98745200-98756000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr10:98745200-98760400	Weak transcription	Primary T cells from cord blood	blood
11	chr10:98745400-98755600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:98745400-98756600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr10:98745400-98757600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:98746400-98755600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:98746400-98758600	Weak transcription	Esophagus	oesophagus
16	chr10:98748200-98758200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr10:98748800-98755800	Weak transcription	Aorta	Aorta
18	chr10:98748800-98757600	Weak transcription	Brain Germinal Matrix	brain
19	chr10:98751200-98755600	Weak transcription	Colon Smooth Muscle	Colon
20	chr10:98751200-98755600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr10:98751600-98755800	Weak transcription	Fetal Stomach	stomach
22	chr10:98751600-98756000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:98751600-98758200	Weak transcription	Placenta	Placenta
24	chr10:98751600-98760200	Weak transcription	A549	lung
25	chr10:98751800-98756200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:98752000-98755400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:98752000-98755600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr10:98752000-98755600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:98752000-98755600	Weak transcription	Osteobl	bone
30	chr10:98752000-98755800	Weak transcription	NH-A	brain
31	chr10:98752000-98756000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr10:98752400-98755600	Weak transcription	NHLF	lung
33	chr10:98752600-98755400	Weak transcription	HSMMtube	muscle
34	chr10:98752600-98755800	Weak transcription	HSMM	muscle
35	chr10:98753000-98755600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:98753000-98755600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:98753000-98755600	Weak transcription	Fetal Lung	lung
38	chr10:98753000-98757400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr10:98753000-98759800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr10:98753000-98760000	Weak transcription	Gastric	stomach
41	chr10:98753000-98762400	Weak transcription	Thymus	Thymus
42	chr10:98753000-98765200	Weak transcription	Brain Hippocampus Middle	brain
43	chr10:98753200-98757200	Weak transcription	Fetal Thymus	thymus
44	chr10:98753800-98756600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr10:98754000-98755200	Enhancers	Psoas Muscle	Psoas
46	chr10:98754000-98757000	Enhancers	Fetal Heart	heart
47	chr10:98754600-98755200	Enhancers	Fetal Intestine Large	intestine
48	chr10:98754600-98756600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:98754600-98756600	Enhancers	Ovary	ovary
50	chr10:98754800-98755400	Weak transcription	Fetal Intestine Small	intestine

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