Variant report

Variant	rs2999523
Chromosome Location	chr1:151949943-151949944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151948065..151950205-chr1:152058703..152061425,2	MCF-7	breast:
2	chr1:151949201..151951606-chr1:152006321..152008860,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1038746	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1038748	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1387834	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1387835	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1473493	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1473494	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1473495	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1532132	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1552605	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1552607	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1602245	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1602246	0.87[EUR][1000 genomes]
rs1602248	0.87[EUR][1000 genomes]
rs17583707	0.82[AMR][1000 genomes]
rs1826170	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1826171	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1826172	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1873311	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2087550	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2338018	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932563	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932564	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932584	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2932585	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2932588	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932591	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932592	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932595	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932596	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2932597	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999509	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999511	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999514	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999515	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999518	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999519	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999520	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999522	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999524	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999525	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999527	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999529	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999530	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2999558	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3007692	0.82[AMR][1000 genomes]
rs3007699	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3007700	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3007701	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3007704	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34370890	0.82[AMR][1000 genomes]
rs61113720	0.82[AMR][1000 genomes]
rs971888	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2999523	S100A10	cis	Adipose Subcutaneous	GTEx
rs2999523	RORC	cis	Whole Blood	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
2	chr1:151939600-151950800	Enhancers	Fetal Intestine Small	intestine
3	chr1:151941000-151953200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151941000-151953200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:151941000-151953400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:151941000-151953400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:151941000-151954800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:151941200-151952800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:151941200-151952800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:151941200-151953000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:151941800-151953000	Weak transcription	Lung	lung
14	chr1:151941800-151953600	Weak transcription	Gastric	stomach
15	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
16	chr1:151942400-151951800	Enhancers	Fetal Intestine Large	intestine
17	chr1:151943000-151953000	Weak transcription	Spleen	Spleen
18	chr1:151945400-151952400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:151945400-151953400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:151945600-151950600	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:151945600-151950800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:151945600-151953000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:151945600-151953600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:151945600-151953800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:151945600-151953800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:151946000-151951200	Enhancers	Hela-S3	cervix
27	chr1:151946000-151952600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:151946000-151954800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:151946000-151954800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:151946200-151952800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:151946200-151953000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:151946200-151953000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr1:151946200-151954800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:151946200-151954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:151946200-151956200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:151946400-151952400	Weak transcription	HSMMtube	muscle
37	chr1:151946600-151957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:151946600-151958800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:151947400-151950800	Enhancers	K562	blood
40	chr1:151947600-151952400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:151947600-151953400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:151947800-151951800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:151948000-151951800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:151948000-151956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:151948400-151951200	Enhancers	HepG2	liver
46	chr1:151948400-151955200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:151948600-151951000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:151948800-151950200	Enhancers	NHEK	skin
49	chr1:151948800-151950600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:151949000-151950000	Enhancers	Muscle Satellite Cultured Cells	--

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