Variant report

Variant	rs66753029
Chromosome Location	chr6:35056852-35056853
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	chr6:35054576..35057054-chr6:35059180..35061237,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11552398	0.84[EUR][1000 genomes]
rs13207848	0.82[EUR][1000 genomes]
rs13208078	0.93[EUR][1000 genomes]
rs13214114	0.82[EUR][1000 genomes]
rs1747516	0.82[EUR][1000 genomes]
rs1747517	0.82[EUR][1000 genomes]
rs17610836	0.84[EUR][1000 genomes]
rs2762336	0.80[EUR][1000 genomes]
rs34208177	0.82[EUR][1000 genomes]
rs35095464	0.82[EUR][1000 genomes]
rs35106671	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270050	0.80[EUR][1000 genomes]
rs57111149	0.82[EUR][1000 genomes]
rs67167177	0.82[EUR][1000 genomes]
rs67941146	0.82[EUR][1000 genomes]
rs6899618	0.82[EUR][1000 genomes]
rs6913286	0.82[EUR][1000 genomes]
rs6913975	0.82[EUR][1000 genomes]
rs6936337	0.82[EUR][1000 genomes]
rs6942104	0.82[EUR][1000 genomes]
rs820061	0.80[EUR][1000 genomes]
rs820062	0.80[EUR][1000 genomes]
rs820063	0.80[EUR][1000 genomes]
rs820065	0.80[EUR][1000 genomes]
rs820066	0.80[EUR][1000 genomes]
rs820067	0.80[EUR][1000 genomes]
rs820069	0.80[EUR][1000 genomes]
rs820099	0.80[EUR][1000 genomes]
rs820100	0.80[EUR][1000 genomes]
rs820103	0.82[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
rs66753029	TCP11	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:119 , 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	chr6:35020400-35059400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:35024800-35062000	Weak transcription	A549	lung
5	chr6:35026600-35059200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:35028600-35060000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:35036200-35059200	Strong transcription	Primary T cells from cord blood	blood
8	chr6:35037000-35061800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:35039400-35060600	Strong transcription	Fetal Intestine Large	intestine
10	chr6:35040000-35057000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:35042200-35059200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:35044400-35058800	Strong transcription	Duodenum Mucosa	Duodenum
13	chr6:35044600-35057600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:35044600-35058200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:35044800-35057800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr6:35044800-35058800	Strong transcription	Gastric	stomach
17	chr6:35044800-35059000	Strong transcription	Left Ventricle	heart
18	chr6:35045000-35057000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:35045000-35057000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:35045000-35057800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr6:35045000-35059000	Strong transcription	Pancreas	Pancrea
22	chr6:35045200-35057000	Strong transcription	Fetal Brain Female	brain
23	chr6:35045200-35057400	Strong transcription	Ovary	ovary
24	chr6:35045200-35057800	Strong transcription	Brain Germinal Matrix	brain
25	chr6:35045200-35059400	Strong transcription	Thymus	Thymus
26	chr6:35045600-35057200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr6:35046400-35057800	Strong transcription	Fetal Lung	lung
28	chr6:35049600-35058800	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr6:35049600-35060200	Weak transcription	Psoas Muscle	Psoas
30	chr6:35050000-35057200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:35050000-35059800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr6:35050000-35063800	Weak transcription	HUVEC	blood vessel
33	chr6:35050200-35059600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr6:35050400-35057000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:35050400-35057400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:35050400-35057400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:35050600-35057400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr6:35050600-35057600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:35050600-35058800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:35050600-35060200	Weak transcription	Right Atrium	heart
41	chr6:35050800-35057600	Strong transcription	Colonic Mucosa	Colon
42	chr6:35051000-35057000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:35051000-35057000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:35051000-35058400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:35051200-35057000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:35051400-35061400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:35051600-35057200	Weak transcription	Fetal Brain Male	brain
48	chr6:35051800-35064000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:35052000-35058200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:35052400-35057000	Strong transcription	Brain Angular Gyrus	brain

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