Variant report

Variant	rs10267854
Chromosome Location	chr7:27857103-27857104
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	chr7:27856504..27859420-chr7:27862843..27864597,2	K562	blood:
2	chr7:27701552..27704256-chr7:27856861..27858548,2	K562	blood:

Variant related genes	Relation type
ENSG00000106049	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10155851	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10225487	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10277437	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10486549	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap]
rs10486559	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10951184	0.82[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12666447	1.00[LWK][hapmap]
rs12668668	1.00[LWK][hapmap]
rs16874364	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16874393	0.90[CEU][hapmap]
rs16874395	0.91[CEU][hapmap]
rs17155537	0.91[CEU][hapmap]
rs17155702	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17155943	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17155950	0.95[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17155969	0.86[CEU][hapmap]
rs17155971	0.86[CEU][hapmap]
rs2051830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2074579	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074769	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2107413	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2108309	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2158388	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2237339	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2237340	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2237341	0.89[EUR][1000 genomes]
rs2285931	0.83[EUR][1000 genomes]
rs2299106	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2391450	0.86[CEU][hapmap]
rs2391488	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3779473	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3940270	0.94[CEU][hapmap];0.83[AMR][1000 genomes]
rs4719907	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4719908	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4722741	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57932688	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58314651	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58857361	0.82[EUR][1000 genomes]
rs62449629	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62449639	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62449640	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62451077	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62451079	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62454806	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62454945	0.82[EUR][1000 genomes]
rs6462048	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6462049	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6462052	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6462053	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6944251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6944913	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6971813	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6972821	0.82[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72598505	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs757136	1.00[LWK][hapmap]
rs759268	0.95[CEU][hapmap]
rs7784038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7801301	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7803019	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7803227	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7809735	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9639563	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2758109	chr7:27793616-27972869	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2759520	chr7:27793616-27972869	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv5677	chr7:27839504-27884505	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1018550	chr7:27844038-27925645	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv3386868	chr7:27856698-27857228	Strong transcription Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10267854	SLC25A4	trans	parietal	SCAN
rs10267854	SNX10	cis	cerebellum	SCAN
rs10267854	ACSL6	trans	parietal	SCAN
rs10267854	PRR15	cis	parietal	SCAN
rs10267854	TAX1BP1	cis	cerebellum	SCAN
rs10267854	HOXA9	cis	parietal	SCAN
rs10267854	SCRN1	cis	cerebellum	SCAN
rs10267854	CRHR2	cis	parietal	SCAN
rs10267854	TRIL	cis	parietal	SCAN
rs10267854	HOXA13	cis	parietal	SCAN
rs10267854	HIBADH	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27781000-27861800	Weak transcription	Aorta	Aorta
2	chr7:27784800-27878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:27790600-27857400	Weak transcription	Colonic Mucosa	Colon
4	chr7:27798600-27874000	Weak transcription	Brain Angular Gyrus	brain
5	chr7:27805800-27857600	Weak transcription	Esophagus	oesophagus
6	chr7:27806000-27882600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:27806400-27878600	Weak transcription	Right Ventricle	heart
8	chr7:27815600-27874000	Weak transcription	Pancreas	Pancrea
9	chr7:27823800-27878000	Weak transcription	Spleen	Spleen
10	chr7:27824200-27876800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:27825600-27874000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:27826000-27870000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:27827000-27881800	Weak transcription	Small Intestine	intestine
14	chr7:27827600-27878400	Weak transcription	Fetal Kidney	kidney
15	chr7:27833000-27858000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:27833600-27858400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:27834400-27873600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:27835200-27857600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:27835200-27878200	Weak transcription	Gastric	stomach
20	chr7:27836400-27867400	Weak transcription	HUVEC	blood vessel
21	chr7:27836400-27878000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:27836400-27882200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr7:27837000-27873800	Weak transcription	Psoas Muscle	Psoas
24	chr7:27837600-27857200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:27840000-27880600	Weak transcription	Hela-S3	cervix
26	chr7:27842400-27877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:27843600-27877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:27847600-27885200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr7:27848400-27871600	Weak transcription	HMEC	breast
30	chr7:27848400-27873400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr7:27848600-27868200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr7:27848600-27871000	Weak transcription	K562	blood
33	chr7:27849200-27873400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:27849800-27860200	Strong transcription	Primary T cells from cord blood	blood
35	chr7:27850200-27860000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr7:27850200-27860600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr7:27850200-27881400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:27850400-27861200	Strong transcription	Placenta	Placenta
39	chr7:27851200-27863800	Strong transcription	Liver	Liver
40	chr7:27851400-27860800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:27851800-27859600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:27852200-27862600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr7:27852800-27858400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:27853000-27868800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr7:27853200-27857800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:27853200-27861000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:27853400-27857600	Weak transcription	Fetal Lung	lung
48	chr7:27853400-27860400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr7:27853400-27864000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:27853600-27862000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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