Variant report

Variant	rs1541519
Chromosome Location	chr7:102466741-102466742
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102459925..102462268-chr7:102466191..102467871,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10227402	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10228495	0.86[ASW][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10233721	0.87[AMR][1000 genomes]
rs10241865	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10242028	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10250490	0.84[ASN][1000 genomes]
rs10257317	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10271157	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10271184	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10273725	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs10279449	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953374	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1100046	0.82[ASN][1000 genomes]
rs11514917	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs11972261	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs11976237	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs11978799	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11981980	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12537977	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12668434	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13233521	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs13242493	0.82[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs1608651	0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs17136090	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2190673	0.81[ASN][1000 genomes]
rs2411046	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs2411056	0.90[ASN][1000 genomes]
rs2430070	0.81[YRI][hapmap]
rs28856331	0.84[ASN][1000 genomes]
rs41501847	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4620204	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs4729860	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs56269620	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57253646	0.94[ASN][1000 genomes]
rs59544295	0.91[ASN][1000 genomes]
rs59709436	0.91[ASN][1000 genomes]
rs6465873	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6465876	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465878	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6465880	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6946773	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6947403	0.86[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs6949391	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6953980	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6960428	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6969054	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975388	0.88[ASN][1000 genomes]
rs7778418	0.95[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs7779145	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7780981	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7782908	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7789252	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7794668	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7800548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804322	0.91[ASN][1000 genomes]
rs847646	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs847647	0.86[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs847648	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs847649	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs847656	0.86[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs847658	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs869332	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs9718453	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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 miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1025363	chr7:102072448-102471485	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	esv2761100	chr7:102335787-102481978	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv608057	chr7:102440184-102538515	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1541519	DPY19L2P2	cis	parietal	SCAN
rs1541519	CUX1	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102416400-102467600	Weak transcription	Brain Anterior Caudate	brain
2	chr7:102421600-102475600	Weak transcription	Fetal Thymus	thymus
3	chr7:102422000-102474800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:102422000-102476000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr7:102439600-102467400	Weak transcription	Thymus	Thymus
6	chr7:102445600-102467600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:102445600-102469200	Weak transcription	Fetal Brain Male	brain
8	chr7:102445800-102467400	Weak transcription	Lung	lung
9	chr7:102446200-102467400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr7:102447000-102469400	Weak transcription	Brain Angular Gyrus	brain
11	chr7:102447200-102467400	Weak transcription	Primary B cells from cord blood	blood
12	chr7:102447200-102469400	Weak transcription	Fetal Brain Female	brain
13	chr7:102447400-102477200	Weak transcription	Psoas Muscle	Psoas
14	chr7:102447800-102467400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:102447800-102473000	Weak transcription	Placenta	Placenta
16	chr7:102448000-102469200	Weak transcription	Right Ventricle	heart
17	chr7:102448000-102479000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:102448200-102470800	Weak transcription	Small Intestine	intestine
19	chr7:102448400-102471800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:102449400-102467400	Weak transcription	Left Ventricle	heart
21	chr7:102449400-102467600	Weak transcription	Fetal Muscle Leg	muscle
22	chr7:102449600-102467400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:102449600-102469400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr7:102450000-102475000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr7:102450200-102475600	Weak transcription	Esophagus	oesophagus
26	chr7:102452000-102480000	Weak transcription	Colon Smooth Muscle	Colon
27	chr7:102452200-102467400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:102452200-102472800	Weak transcription	HSMMtube	muscle
29	chr7:102452400-102469400	Weak transcription	Adipose Nuclei	Adipose
30	chr7:102454000-102467800	Weak transcription	Fetal Kidney	kidney
31	chr7:102454200-102469400	Weak transcription	HepG2	liver
32	chr7:102454200-102484600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr7:102454400-102469600	Weak transcription	Aorta	Aorta
34	chr7:102454400-102475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:102454600-102475000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:102454600-102475600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr7:102454800-102467400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:102454800-102467600	Weak transcription	Fetal Stomach	stomach
39	chr7:102454800-102473200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:102455000-102467600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:102455000-102467800	Weak transcription	HMEC	breast
42	chr7:102455000-102469600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:102455000-102475000	Weak transcription	NHLF	lung
44	chr7:102455000-102475000	Weak transcription	Osteobl	bone
45	chr7:102455200-102467400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:102455200-102469400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr7:102455200-102472800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:102455600-102469200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:102455600-102473200	Weak transcription	HSMM	muscle
50	chr7:102456000-102469200	Weak transcription	Pancreas	Pancrea

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