Variant report

Variant	rs13208078
Chromosome Location	chr6:35059791-35059792
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	chr6:35040084..35042469-chr6:35059564..35062383,2	MCF-7	breast:
2	chr6:35054576..35057054-chr6:35059180..35061237,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1093986	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11552398	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11961798	0.91[CEU][hapmap];0.96[YRI][hapmap]
rs11964930	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs11969000	0.85[CEU][hapmap]
rs13196771	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13199238	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs13203612	0.81[CEU][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13206654	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13207848	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs13211490	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs13214114	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13217848	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs16871749	0.92[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16871809	0.92[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16871814	0.92[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1747516	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1747517	0.92[CEU][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17610836	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2234044	0.92[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2234045	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs2395608	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2395610	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs2762336	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34103100	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34208177	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34250961	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34715060	0.80[EUR][1000 genomes]
rs34930033	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35095464	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35106671	0.87[EUR][1000 genomes]
rs35693439	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3756856	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs41270050	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4628094	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57111149	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66579470	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66753029	0.93[EUR][1000 genomes]
rs67167177	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67638810	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67941146	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6899618	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6906666	0.92[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6913286	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6913975	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6915649	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs6926532	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6936337	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6942104	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs728238	0.91[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72897804	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7766770	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7767073	0.92[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs820061	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820062	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820063	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820065	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820066	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820067	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820069	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820095	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs820099	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820100	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs820101	0.82[EUR][1000 genomes]
rs820103	0.92[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9462053	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9462054	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9469950	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv869750	chr6:35031548-35085585	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13208078	TCP11	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35018800-35060600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:35020000-35059800	Strong transcription	Fetal Intestine Small	intestine
3	chr6:35024800-35062000	Weak transcription	A549	lung
4	chr6:35028600-35060000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:35037000-35061800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:35039400-35060600	Strong transcription	Fetal Intestine Large	intestine
7	chr6:35049600-35060200	Weak transcription	Psoas Muscle	Psoas
8	chr6:35050000-35059800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:35050000-35063800	Weak transcription	HUVEC	blood vessel
10	chr6:35050600-35060200	Weak transcription	Right Atrium	heart
11	chr6:35051400-35061400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:35051800-35064000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:35052800-35060000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:35053400-35060200	Weak transcription	Fetal Kidney	kidney
15	chr6:35053400-35064200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:35054000-35060000	Genic enhancers	Placenta	Placenta
17	chr6:35054000-35063800	Weak transcription	Stomach Mucosa	stomach
18	chr6:35055000-35064000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:35055200-35059800	Genic enhancers	Adipose Nuclei	Adipose
20	chr6:35055400-35060600	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr6:35055600-35061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:35055800-35061000	Weak transcription	Primary B cells from cord blood	blood
23	chr6:35055800-35064000	Weak transcription	NHEK	skin
24	chr6:35056000-35061600	Weak transcription	Small Intestine	intestine
25	chr6:35056200-35061000	Genic enhancers	Fetal Stomach	stomach
26	chr6:35056200-35061000	Enhancers	HMEC	breast
27	chr6:35056200-35061800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:35056400-35061400	Weak transcription	Hela-S3	cervix
29	chr6:35056600-35059800	Genic enhancers	HSMMtube	muscle
30	chr6:35056600-35060400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:35056600-35060800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr6:35056600-35064000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:35056600-35064000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:35056600-35064200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:35056800-35060000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:35056800-35061600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:35056800-35063400	Weak transcription	Brain Anterior Caudate	brain
38	chr6:35057000-35060400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:35057000-35060800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:35057000-35061600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:35057000-35061600	Weak transcription	HepG2	liver
42	chr6:35057000-35063400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:35057000-35063800	Weak transcription	Brain Angular Gyrus	brain
44	chr6:35057200-35062200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:35057200-35062600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:35057200-35062800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:35057200-35062800	Enhancers	NHDF-Ad	bronchial
48	chr6:35057400-35061000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:35057400-35061600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr6:35057400-35062200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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