Variant report

Variant	rs11885942
Chromosome Location	chr2:100004165-100004166
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	chr2:99952493..99955462-chr2:100001894..100004691,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10496336	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11887935	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11893359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11896520	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12053372	0.82[CEU][hapmap]
rs12466114	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12474305	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12479064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17760953	0.82[CEU][hapmap]
rs1823569	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1922624	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2141907	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2305352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28369945	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28369960	0.80[ASN][1000 genomes]
rs28382977	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792143	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341989	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4851203	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851207	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4851210	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61436115	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153852	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62155769	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62155807	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6714650	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737094	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs995617	0.82[CEU][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11885942	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs11885942	LYG1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
2	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
3	chr2:99976200-100004400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:99976600-100004800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
6	chr2:99979400-100004200	Strong transcription	Fetal Thymus	thymus
7	chr2:99979600-100009600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:99985600-100006800	Weak transcription	Colonic Mucosa	Colon
10	chr2:99990000-100006600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:99990000-100012200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:99990200-100010800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:99990600-100006600	Weak transcription	Pancreas	Pancrea
14	chr2:99990600-100010800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:99990600-100010800	Weak transcription	Spleen	Spleen
16	chr2:99990800-100004600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:99990800-100007000	Weak transcription	Gastric	stomach
18	chr2:99993200-100006600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:99994200-100010000	Weak transcription	Brain Substantia Nigra	brain
20	chr2:99994200-100010800	Weak transcription	Fetal Brain Male	brain
21	chr2:99994200-100011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:99996600-100009400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:99996800-100010000	Weak transcription	Small Intestine	intestine
24	chr2:99997200-100009000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:99997200-100011000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:99998800-100007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:99999000-100006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:99999200-100008800	Strong transcription	HepG2	liver
29	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:99999600-100006600	Weak transcription	HMEC	breast
31	chr2:100000000-100006000	Weak transcription	HUVEC	blood vessel
32	chr2:100000000-100014800	Weak transcription	Psoas Muscle	Psoas
33	chr2:100000200-100006200	Weak transcription	Hela-S3	cervix
34	chr2:100000200-100006600	Weak transcription	NHEK	skin
35	chr2:100000200-100007000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:100000400-100005200	Weak transcription	HSMM	muscle
37	chr2:100000400-100006600	Weak transcription	Brain Anterior Caudate	brain
38	chr2:100000400-100006800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:100000400-100007000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:100000400-100009400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:100001000-100004400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:100001000-100005600	Weak transcription	NHDF-Ad	bronchial
43	chr2:100001000-100007000	Weak transcription	Fetal Kidney	kidney
44	chr2:100001000-100022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr2:100001200-100005400	Weak transcription	Osteobl	bone
46	chr2:100001200-100006400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:100001200-100006600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:100001200-100006600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:100001200-100007000	Weak transcription	Brain Germinal Matrix	brain
50	chr2:100001200-100007000	Weak transcription	Brain Inferior Temporal Lobe	brain

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