Variant report

Variant	rs4709112
Chromosome Location	chr6:166751839-166751840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:166751664..166755250-chr6:166772904..166776274,3	K562	blood:
2	chr6:166748322..166751240-chr6:166751244..166753150,2	MCF-7	breast:
3	chr6:166751804..166757558-chr6:166793969..166799153,5	K562	blood:
4	chr6:166750705..166753304-chr6:166793796..166795469,2	K562	blood:
5	chr6:166698710..166701539-chr6:166750702..166753192,3	K562	blood:
6	chr6:166750967..166754365-chr6:166755785..166758738,3	MCF-7	breast:
7	chr6:166751208..166754791-chr6:166757264..166760335,3	MCF-7	breast:
8	chr6:166751051..166752685-chr6:166755340..166756896,2	MCF-7	breast:
9	chr6:166751783..166754110-chr6:166780871..166783189,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261420	Chromatin interaction
ENSG00000060762	Chromatin interaction
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10806847	0.95[CEU][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10862	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11168	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1997661	0.85[ASN][1000 genomes]
rs2343590	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4470829	0.96[EUR][1000 genomes]
rs4598048	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4710041	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6902813	0.85[ASN][1000 genomes]
rs6905635	1.00[CHB][hapmap]
rs6909951	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918091	0.81[ASN][1000 genomes]
rs6918901	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6927168	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs735297	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs7744743	0.81[ASN][1000 genomes]
rs7757549	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9355572	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9355574	0.81[ASN][1000 genomes]
rs9356476	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9356478	1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9356479	0.88[AMR][1000 genomes]
rs9366005	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9366006	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9366007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9459654	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4709112	SFT2D1	cis	lymphoblastoid	seeQTL
rs4709112	HNRNPA1P49	cis	lung	GTEx
rs4709112	SFT2D1	cis	Whole Blood	GTEx
rs4709112	LOC441177	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
2	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
3	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
4	chr6:166738200-166754200	Weak transcription	NH-A	brain
5	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
8	chr6:166744400-166752000	Weak transcription	Right Atrium	heart
9	chr6:166744400-166754800	Weak transcription	NHDF-Ad	bronchial
10	chr6:166745400-166754400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:166745400-166755000	Weak transcription	A549	lung
12	chr6:166745800-166752200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:166746000-166752000	Strong transcription	Fetal Intestine Large	intestine
14	chr6:166746200-166752800	Strong transcription	Fetal Intestine Small	intestine
15	chr6:166746200-166753800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:166746200-166754800	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr6:166746400-166752600	Genic enhancers	Spleen	Spleen
18	chr6:166746600-166752400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:166747000-166753400	Weak transcription	Fetal Brain Male	brain
20	chr6:166747200-166752000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:166747200-166754600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:166747400-166752000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:166747600-166753000	Strong transcription	Fetal Muscle Leg	muscle
24	chr6:166747600-166753800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:166747600-166754000	Strong transcription	Fetal Stomach	stomach
26	chr6:166747800-166755000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr6:166748000-166752000	Weak transcription	Pancreas	Pancrea
28	chr6:166748000-166752000	Genic enhancers	Dnd41	blood
29	chr6:166748000-166752400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:166748000-166753000	Strong transcription	K562	blood
31	chr6:166748000-166754000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:166748200-166752000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:166748200-166752000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:166748200-166752000	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr6:166748200-166752000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:166748200-166752000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr6:166748200-166752400	Strong transcription	Primary B cells from cord blood	blood
38	chr6:166748200-166752400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:166748200-166752800	Weak transcription	Small Intestine	intestine
40	chr6:166748200-166754400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:166748200-166754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:166748400-166752200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:166748400-166752400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr6:166748400-166754600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:166748600-166753200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:166748600-166753800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:166748800-166752000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:166749000-166752000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:166749200-166752000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:166749400-166754000	Weak transcription	Osteobl	bone

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