Variant report

Variant	rs820077
Chromosome Location	chr6:35033854-35033855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35027834..35029968-chr6:35032421..35033978,2	K562	blood:
2	chr6:35011986..35013703-chr6:35031904..35034159,2	K562	blood:
3	chr6:35027834..35030317-chr6:35032384..35033921,2	K562	blood:
4	chr6:35032635..35034931-chr6:35037985..35040100,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1093985	0.86[AFR][1000 genomes]
rs1093986	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11552398	0.88[CHD][hapmap]
rs13203612	0.82[AMR][1000 genomes]
rs13206654	0.82[AMR][1000 genomes]
rs13207848	0.84[CHB][hapmap]
rs13214114	0.82[AMR][1000 genomes]
rs13216424	0.94[CHD][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16871749	0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs16871809	0.88[CHD][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs16871814	0.88[CHD][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs16896559	0.84[CHB][hapmap]
rs1747516	0.82[AMR][1000 genomes]
rs1747517	0.82[AMR][1000 genomes]
rs1880090	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs2177380	0.84[CHB][hapmap]
rs2234044	0.88[CHD][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs2762336	0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34103100	0.82[AMR][1000 genomes]
rs34208177	0.82[AMR][1000 genomes]
rs34250961	0.82[AMR][1000 genomes]
rs35095464	0.82[AMR][1000 genomes]
rs3756856	0.88[CHD][hapmap]
rs41270050	0.82[AMR][1000 genomes]
rs4628094	0.82[AMR][1000 genomes]
rs57111149	0.82[AMR][1000 genomes]
rs66579470	0.82[AMR][1000 genomes]
rs67167177	0.82[AMR][1000 genomes]
rs67638810	0.82[AMR][1000 genomes]
rs67941146	0.82[AMR][1000 genomes]
rs6899618	0.82[AMR][1000 genomes]
rs6906666	0.88[CHD][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs6913286	0.82[AMR][1000 genomes]
rs6913975	0.82[AMR][1000 genomes]
rs6926532	0.82[AMR][1000 genomes]
rs72537461	0.81[AFR][1000 genomes]
rs728238	0.82[AMR][1000 genomes]
rs7766770	0.82[AMR][1000 genomes]
rs7767073	0.82[AMR][1000 genomes]
rs820061	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs820062	0.84[CHB][hapmap];0.94[CHD][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs820063	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs820065	0.88[CHD][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs820066	0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs820067	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs820068	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs820069	0.84[CHB][hapmap];0.94[CHD][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs820072	0.82[ASN][1000 genomes]
rs820088	0.84[AFR][1000 genomes]
rs820095	0.84[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs820098	0.82[YRI][hapmap]
rs820099	0.82[CHD][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes]
rs820100	0.85[AMR][1000 genomes]
rs820103	0.82[AMR][1000 genomes]
rs865352	0.97[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs820077	TCP11	cis	lymphoblastoid	seeQTL
rs820077	TULP1	cis	cerebellum	SCAN
rs820077	DEF6	cis	multi-tissue	Pritchard
rs820077	BRPF3	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34994600-35036000	Weak transcription	K562	blood
2	chr6:35015800-35044200	Weak transcription	HMEC	breast
3	chr6:35016200-35055000	Weak transcription	Hela-S3	cervix
4	chr6:35017600-35036200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:35017800-35053000	Weak transcription	Small Intestine	intestine
6	chr6:35018400-35052800	Weak transcription	Fetal Kidney	kidney
7	chr6:35018600-35051000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:35018800-35038200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr6:35018800-35060600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:35020000-35059800	Strong transcription	Fetal Intestine Small	intestine
11	chr6:35020200-35037600	Strong transcription	Fetal Intestine Large	intestine
12	chr6:35020400-35059400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:35020600-35034800	Strong transcription	Primary T cells from cord blood	blood
14	chr6:35021000-35037000	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:35021000-35037600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:35021200-35034800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr6:35021400-35036200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:35021400-35037400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:35021600-35036800	Strong transcription	Colonic Mucosa	Colon
20	chr6:35021800-35055400	Weak transcription	HSMM	muscle
21	chr6:35022000-35034800	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr6:35022000-35036600	Strong transcription	Placenta	Placenta
23	chr6:35022400-35036200	Strong transcription	Pancreas	Pancrea
24	chr6:35022600-35037200	Strong transcription	Gastric	stomach
25	chr6:35024000-35039200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:35024600-35034800	Strong transcription	Ovary	ovary
27	chr6:35024600-35035400	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:35024800-35062000	Weak transcription	A549	lung
29	chr6:35025200-35037400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:35025600-35056000	Strong transcription	Liver	Liver
31	chr6:35025800-35035400	Strong transcription	HSMMtube	muscle
32	chr6:35026400-35034600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:35026400-35036000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr6:35026400-35036400	Strong transcription	Fetal Stomach	stomach
35	chr6:35026600-35059200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr6:35027600-35036400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:35028400-35048800	Weak transcription	Psoas Muscle	Psoas
38	chr6:35028600-35060000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:35028800-35036200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:35028800-35045400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:35029000-35036000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:35029000-35046200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:35029000-35050800	Weak transcription	NHLF	lung
44	chr6:35029200-35034400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:35029200-35036200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:35029200-35039800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:35029200-35045800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:35029200-35046400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:35029400-35035200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:35029400-35035400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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