Variant report

Variant	rs10249326
Chromosome Location	chr7:107016421-107016422
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	chr3:5237281..5239689-chr7:107015732..107018520,2	MCF-7	breast:
2	chr7:107008875..107010473-chr7:107014803..107016730,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1015410	0.88[CEU][hapmap]
rs1024401	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10260250	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap]
rs10264687	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1034734	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11761775	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs12532293	0.81[EUR][1000 genomes]
rs1468335	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2107762	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2107763	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2158347	0.92[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap]
rs2189500	0.81[EUR][1000 genomes]
rs2214679	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2237663	0.80[ASN][1000 genomes]
rs2237667	0.92[CEU][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2250410	0.81[CEU][hapmap]
rs2269970	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2395839	0.88[CEU][hapmap]
rs2520279	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs2712192	0.89[CEU][hapmap]
rs2712194	0.88[CEU][hapmap]
rs28718577	0.80[EUR][1000 genomes]
rs4727674	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4727675	0.93[EUR][1000 genomes]
rs4727682	0.81[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4730243	0.82[EUR][1000 genomes]
rs4730244	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs57784799	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57815418	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466163	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6466164	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6466165	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6954422	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs6966616	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs6971864	0.92[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap]
rs7357192	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7787113	0.89[CEU][hapmap]
rs7789927	0.83[EUR][1000 genomes]
rs7791955	0.85[CEU][hapmap]
rs7794142	0.80[EUR][1000 genomes]
rs7794437	0.80[EUR][1000 genomes]
rs7794896	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7802375	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7804398	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv608073	chr7:106960515-107063686	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10249326	LHFPL3	cis	parietal	SCAN
rs10249326	COG5	cis	cerebellum	SCAN
rs10249326	PSMC2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106989200-107018800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:107001400-107024600	Weak transcription	Lung	lung
3	chr7:107001400-107026800	Weak transcription	Aorta	Aorta
4	chr7:107001400-107027200	Weak transcription	Right Ventricle	heart
5	chr7:107001400-107031200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:107001400-107037600	Weak transcription	Spleen	Spleen
7	chr7:107001400-107053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:107002400-107024200	Weak transcription	Fetal Intestine Small	intestine
9	chr7:107002600-107027000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:107002800-107024600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:107002800-107027400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:107002800-107027600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:107003000-107026800	Weak transcription	Fetal Muscle Leg	muscle
14	chr7:107003000-107027000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:107003200-107024600	Weak transcription	Left Ventricle	heart
16	chr7:107003200-107031400	Weak transcription	Fetal Intestine Large	intestine
17	chr7:107003400-107019000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:107003400-107027200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr7:107003600-107023800	Weak transcription	Primary B cells from cord blood	blood
20	chr7:107003600-107025000	Weak transcription	K562	blood
21	chr7:107003600-107045000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:107003800-107038800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:107003800-107048400	Weak transcription	Dnd41	blood
24	chr7:107003800-107050200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:107004400-107019600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr7:107005200-107025200	Weak transcription	Primary T cells from cord blood	blood
27	chr7:107006600-107027600	Weak transcription	HMEC	breast
28	chr7:107008400-107048200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:107013200-107038600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:107013600-107027200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:107014200-107027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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