Variant report

Variant	rs10946160
Chromosome Location	chr6:166757818-166757819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr6:166757818-166757998	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:166757801-166758016	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:166755072-166758044	K562	blood:	n/a	n/a
4	EP300	chr6:166757702-166757997	K562	blood:	n/a	n/a
5	JUND	chr6:166757716-166758030	K562	blood:	n/a	n/a
6	ATF3	chr6:166757713-166757981	K562	blood:	n/a	n/a
7	POLR2A	chr6:166757573-166758057	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:166757659-166757869	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:166753320..166757958-chr6:166794622..166799153,8	K562	blood:
2	chr6:166751208..166754791-chr6:166757264..166760335,3	MCF-7	breast:
3	chr6:166719852..166722547-chr6:166755922..166758056,2	K562	blood:
4	chr6:166756132..166758070-chr6:166759956..166762577,2	MCF-7	breast:

No data

Variant related genes	Relation type
SFT2D1	TF binding region
ENSG00000060762	Chromatin interaction
ENSG00000261420	Chromatin interaction
ENSG00000176381	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10455809	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10455976	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10455977	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10455978	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10946152	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10946158	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10946161	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11551053	0.85[ASN][1000 genomes]
rs11752886	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11753652	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11755305	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]
rs12198613	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209616	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12214281	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214812	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12662924	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599841	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2294333	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294334	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294335	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144886	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4144887	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4144888	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55936781	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59337176	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66461381	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68016351	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6932631	0.91[CEU][hapmap]
rs73030701	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73263155	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73788236	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7753161	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7771603	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs941683	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10946160	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166756800-166758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:166756800-166758600	Enhancers	Placenta	Placenta
3	chr6:166757000-166758000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:166757000-166758000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:166757000-166758400	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:166757000-166765200	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:166757000-166765400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:166757000-166779200	Weak transcription	Right Atrium	heart
9	chr6:166757200-166758000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:166757200-166758400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:166757200-166760000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:166757200-166761000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:166757400-166758000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:166757400-166759200	Enhancers	K562	blood
15	chr6:166757400-166759800	Weak transcription	Liver	Liver
16	chr6:166757400-166760000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr6:166757400-166760400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:166757400-166762600	Enhancers	HepG2	liver
19	chr6:166757600-166758600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:166757600-166759800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:166757800-166758000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell

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