Variant report

Variant	rs6741277
Chromosome Location	chr2:97294903-97294904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97292796..97298372-chr2:97302534..97305789,7	MCF-7	breast:
2	chr2:97288040..97290630-chr2:97292751..97295463,2	MCF-7	breast:
3	chr2:97292666..97295153-chr2:97348242..97350372,2	MCF-7	breast:
4	chr2:97274515..97276731-chr2:97293926..97295461,2	K562	blood:
5	chr2:97294069..97296283-chr2:97297649..97299924,3	MCF-7	breast:
6	chr2:97216820..97219000-chr2:97293306..97295394,2	K562	blood:

Variant related genes	Relation type
ENSG00000114982	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10177168	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693625	1.00[MKK][hapmap]
rs11891926	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17634791	0.84[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1866444	0.86[CEU][hapmap];0.83[CHB][hapmap];0.97[TSI][hapmap]
rs2438712	0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2579498	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2579501	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs2579503	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[CHB][hapmap];0.97[TSI][hapmap]
rs2579506	0.87[CEU][hapmap]
rs4907200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6576974	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576976	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576978	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[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753926	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6741277	TMEM127	cis	parietal	SCAN
rs6741277	HOXB2	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97258200-97302800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:97261200-97301600	Strong transcription	Fetal Thymus	thymus
3	chr2:97275000-97298600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:97283000-97296400	Weak transcription	Psoas Muscle	Psoas
5	chr2:97285200-97296600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:97285400-97296800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:97285400-97302400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:97285600-97295400	Weak transcription	NHLF	lung
9	chr2:97285600-97296400	Weak transcription	Gastric	stomach
10	chr2:97285600-97296800	Weak transcription	Colonic Mucosa	Colon
11	chr2:97285800-97296400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:97285800-97300400	Weak transcription	Right Ventricle	heart
13	chr2:97285800-97302800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:97286400-97296400	Weak transcription	Fetal Brain Male	brain
15	chr2:97287800-97296800	Strong transcription	Dnd41	blood
16	chr2:97288400-97301800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:97288800-97298000	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:97288800-97298000	Weak transcription	Right Atrium	heart
19	chr2:97289000-97300800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:97289200-97295800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:97289600-97301400	Strong transcription	Fetal Intestine Large	intestine
22	chr2:97289800-97298600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:97290000-97295800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:97291000-97298400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:97291000-97302000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:97292000-97296000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:97292200-97298000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:97292200-97301400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:97292200-97301800	Weak transcription	Stomach Mucosa	stomach
30	chr2:97292200-97302400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:97292200-97302400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:97292200-97302600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:97292400-97302200	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:97292600-97297400	Strong transcription	A549	lung
35	chr2:97292600-97299800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:97292600-97300600	Strong transcription	Brain Germinal Matrix	brain
37	chr2:97292600-97301000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr2:97292600-97301400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:97292600-97301400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr2:97292800-97297000	Strong transcription	NH-A	brain
41	chr2:97292800-97298600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:97292800-97300400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:97292800-97301200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:97292800-97302000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:97293000-97297600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:97293000-97298000	Strong transcription	HepG2	liver
47	chr2:97293000-97300600	Strong transcription	Thymus	Thymus
48	chr2:97293000-97301200	Strong transcription	Fetal Stomach	stomach
49	chr2:97293200-97295200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:97293200-97296400	Strong transcription	Liver	Liver

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