Variant report

Variant	rs11755305
Chromosome Location	chr6:166755275-166755276
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:166751804..166757558-chr6:166793969..166799153,5	K562	blood:
2	chr6:166754173..166757774-chr6:166795355..166798060,3	MCF-7	breast:
3	chr6:166753320..166757958-chr6:166794622..166799153,8	K562	blood:

Variant related genes	Relation type
ENSG00000261420	Chromatin interaction
ENSG00000060762	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10455809	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455976	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10455977	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10455978	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946152	0.83[EUR][1000 genomes]
rs10946158	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946160	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10946161	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11551053	0.92[ASN][1000 genomes]
rs11752886	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11753652	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12198613	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12209616	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12214281	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12214812	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12662924	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599841	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294333	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2294334	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294335	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4144886	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4144887	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4144888	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4709111	0.87[CHB][hapmap]
rs4710042	0.87[CHB][hapmap]
rs55936781	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59337176	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66461381	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68016351	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6932631	0.91[CEU][hapmap]
rs73030701	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73263155	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73788236	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7753161	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7767887	0.86[ASN][1000 genomes]
rs7771603	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348119	0.83[CHB][hapmap]
rs9348121	0.87[CHB][hapmap]
rs941683	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS 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	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11755305		cis	Lymphoblastoid	GTEx
rs11755305	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL
rs11755305	LOC401284	cis	multi-tissue	Pritchard
rs11755305	LOC135043	cis	multi-tissue	Pritchard
rs11755305	SFT2D1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:166752800-166755400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:166753400-166755400	Enhancers	Small Intestine	intestine
4	chr6:166753400-166755800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr6:166754200-166755400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:166754600-166755400	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr6:166754600-166755400	Flanking Active TSS	Dnd41	blood
8	chr6:166754600-166755600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:166754600-166756600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:166754600-166756600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:166754600-166756800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:166754600-166756800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:166754600-166756800	Active TSS	GM12878-XiMat	blood
14	chr6:166754800-166755400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr6:166754800-166755400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr6:166754800-166755400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:166754800-166755400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr6:166754800-166755400	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr6:166754800-166755400	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr6:166754800-166755400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr6:166754800-166755400	Flanking Active TSS	Fetal Thymus	thymus
22	chr6:166754800-166755400	Flanking Active TSS	K562	blood
23	chr6:166754800-166755600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:166754800-166755600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr6:166754800-166755600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:166754800-166755600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:166754800-166755600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr6:166754800-166755600	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr6:166754800-166755800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:166754800-166756200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:166754800-166756400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:166754800-166756600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:166754800-166756600	Active TSS	Hela-S3	cervix
34	chr6:166754800-166757000	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr6:166754800-166757000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:166754800-166757000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:166754800-166757000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:166754800-166757000	Active TSS	Colonic Mucosa	Colon
39	chr6:166754800-166757200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:166755000-166755400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:166755000-166755400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr6:166755000-166755400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr6:166755000-166755400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:166755000-166755400	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr6:166755000-166755400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:166755000-166755400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr6:166755000-166755400	Flanking Active TSS	Fetal Heart	heart
48	chr6:166755000-166755400	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr6:166755000-166755400	Flanking Active TSS	Fetal Kidney	kidney
50	chr6:166755000-166755400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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