Variant report

Variant	rs7169
Chromosome Location	chr1:113455099-113455100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113448232..113450362-chr1:113454684..113457292,4	K562	blood:
2	chr1:113453403..113455887-chr1:113526487..113529032,2	MCF-7	breast:
3	chr1:113445118..113448523-chr1:113453652..113455842,3	MCF-7	breast:
4	chr1:113454752..113456463-chr1:113462792..113464691,2	K562	blood:
5	chr1:113453716..113456463-chr1:113462131..113464691,2	K562	blood:
6	chr1:113452222..113455252-chr1:113457293..113459554,4	K562	blood:
7	chr1:113453527..113457019-chr1:113457293..113460216,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10158127	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1049434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776763	0.95[ASN][1000 genomes]
rs10857980	0.96[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs10857982	0.93[ASN][1000 genomes]
rs10857983	0.94[ASN][1000 genomes]
rs11102562	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11102565	0.93[ASN][1000 genomes]
rs11102568	0.88[ASN][1000 genomes]
rs12028967	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12037621	0.92[ASN][1000 genomes]
rs1216603	0.84[EUR][1000 genomes]
rs1539624	0.96[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1629027	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1728218	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1728219	0.80[EUR][1000 genomes]
rs1728232	0.80[EUR][1000 genomes]
rs1983929	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2096301	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2105388	0.93[EUR][1000 genomes]
rs2996295	0.87[ASW][hapmap];0.83[MEX][hapmap]
rs3789592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4301628	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4838969	0.87[EUR][1000 genomes]
rs4838970	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4839273	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6537762	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6537764	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537765	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6663872	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670224	0.90[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6681037	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6681552	0.93[EUR][1000 genomes]
rs7551223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773430	0.82[EUR][1000 genomes]
rs773432	0.82[EUR][1000 genomes]
rs773433	0.82[EUR][1000 genomes]
rs773434	0.81[EUR][1000 genomes]
rs773435	0.82[EUR][1000 genomes]
rs773436	0.81[EUR][1000 genomes]
rs773439	0.80[EUR][1000 genomes]
rs773442	0.84[EUR][1000 genomes]
rs9633370	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers 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	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription 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 target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7169	LRIG2	cis	cerebellum	SCAN
rs7169	OLFML3	cis	cerebellum	SCAN
rs7169	AMPD1	cis	parietal	SCAN
rs7169	DENND2C	cis	parietal	SCAN
rs7169	OVGP1	cis	cerebellum	SCAN
rs7169	SLC6A17	cis	parietal	SCAN
rs7169	DENND2C	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113439200-113459200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:113439200-113460400	Weak transcription	Aorta	Aorta
3	chr1:113440200-113456400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:113440400-113459600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:113444400-113456600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:113446000-113456600	Weak transcription	Fetal Heart	heart
7	chr1:113446200-113455600	Weak transcription	A549	lung
8	chr1:113446400-113457800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:113446600-113459600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:113446800-113459800	Weak transcription	Psoas Muscle	Psoas
11	chr1:113447200-113455400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:113447200-113456000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:113447200-113456400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:113447400-113459200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:113447400-113459600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:113447600-113456200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:113447800-113457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:113447800-113458000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:113447800-113459600	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:113447800-113470200	Weak transcription	Fetal Kidney	kidney
21	chr1:113448200-113457800	Weak transcription	Ovary	ovary
22	chr1:113448400-113457800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:113448600-113457600	Weak transcription	NHDF-Ad	bronchial
24	chr1:113448800-113455600	Weak transcription	GM12878-XiMat	blood
25	chr1:113448800-113458600	Weak transcription	Fetal Stomach	stomach
26	chr1:113448800-113459400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:113449000-113455200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:113449000-113455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:113449000-113456200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:113449000-113456400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:113449000-113456400	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:113449000-113456400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:113449000-113456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:113449000-113457800	Weak transcription	Left Ventricle	heart
35	chr1:113449000-113457800	Weak transcription	Right Ventricle	heart
36	chr1:113449000-113457800	Weak transcription	NHLF	lung
37	chr1:113449000-113458000	Weak transcription	Primary B cells from cord blood	blood
38	chr1:113449000-113458000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:113449000-113458000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:113449000-113460400	Weak transcription	Fetal Lung	lung
41	chr1:113449000-113465600	Weak transcription	Placenta	Placenta
42	chr1:113449000-113466000	Weak transcription	Esophagus	oesophagus
43	chr1:113449000-113468400	Weak transcription	Lung	lung
44	chr1:113449200-113457800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:113449200-113458000	Weak transcription	NH-A	brain
46	chr1:113449200-113458200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:113449600-113455800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:113449600-113455800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:113449600-113456200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:113449600-113457600	Weak transcription	Osteobl	bone

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