Variant report

Variant	rs4706458
Chromosome Location	chr6:71382765-71382766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:71275231..71277384-chr6:71382265..71384787,2	MCF-7	breast:
2	chr6:71377384..71379591-chr6:71381259..71383057,2	MCF-7	breast:
3	chr6:71381415..71384047-chr6:71386712..71389077,2	MCF-7	breast:
4	chr6:71368254..71371028-chr6:71381967..71383874,2	K562	blood:
5	chr6:71375618..71379397-chr6:71381034..71384241,6	K562	blood:

Variant related genes	Relation type
ENSG00000112305	Chromatin interaction
ENSG00000154079	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10498874	0.85[MEX][hapmap]
rs10498876	0.81[MEX][hapmap]
rs10755541	0.85[MEX][hapmap]
rs10755543	0.81[MEX][hapmap]
rs1084388	0.85[MEX][hapmap]
rs10945243	0.85[MEX][hapmap]
rs10945246	0.81[MEX][hapmap]
rs10945247	0.81[MEX][hapmap]
rs12198750	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12202909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203399	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];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12212629	0.85[MEX][hapmap]
rs12215757	0.85[MEX][hapmap]
rs12215835	0.81[MEX][hapmap]
rs13174	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1333966	1.00[ASW][hapmap]
rs1333967	0.81[MEX][hapmap]
rs1577108	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[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1577110	0.85[MEX][hapmap]
rs1716007	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs17763188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1855437	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347433	0.85[MEX][hapmap]
rs2460689	0.81[MEX][hapmap]
rs2474913	0.81[MEX][hapmap]
rs2474917	0.85[MEX][hapmap]
rs2504756	0.81[MEX][hapmap]
rs2504757	0.85[MEX][hapmap]
rs4613778	0.81[MEX][hapmap]
rs4706462	0.81[MEX][hapmap]
rs4706464	0.81[MEX][hapmap]
rs4707843	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707847	0.80[MEX][hapmap]
rs4707851	0.85[MEX][hapmap]
rs4707854	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707855	0.81[MEX][hapmap]
rs615526	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes]
rs7451673	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760267	0.81[MEX][hapmap]
rs7771674	0.81[MEX][hapmap]
rs781967	0.85[MEX][hapmap]
rs781968	0.85[MEX][hapmap]
rs781969	0.81[MEX][hapmap]
rs781977	0.81[MEX][hapmap]
rs781978	0.81[MEX][hapmap]
rs781982	0.81[MEX][hapmap]
rs781983	0.81[MEX][hapmap]
rs781987	0.81[MEX][hapmap]
rs781989	0.85[MEX][hapmap]
rs781990	0.81[MEX][hapmap]
rs9364097	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9455215	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4706458	FAM135A	cis	cerebellum	SCAN
rs4706458	OGFRL1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71378400-71382800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:71378600-71382800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:71378600-71383200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:71378600-71383400	Weak transcription	Aorta	Aorta
5	chr6:71378600-71386600	Weak transcription	Ovary	ovary
6	chr6:71378800-71382800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:71378800-71383000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:71379000-71383600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:71379000-71383600	Enhancers	Small Intestine	intestine
10	chr6:71379200-71382800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:71379200-71382800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:71379200-71382800	Weak transcription	HSMMtube	muscle
13	chr6:71379200-71383200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:71379200-71383200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:71379200-71384000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:71379200-71386200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:71379400-71382800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:71379400-71382800	Weak transcription	Colonic Mucosa	Colon
19	chr6:71379400-71382800	Weak transcription	NH-A	brain
20	chr6:71379400-71382800	Weak transcription	NHLF	lung
21	chr6:71379400-71383000	Enhancers	HepG2	liver
22	chr6:71379400-71383000	Weak transcription	HSMM	muscle
23	chr6:71379400-71383200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:71379400-71383400	Weak transcription	HMEC	breast
25	chr6:71379400-71386000	Weak transcription	Hela-S3	cervix
26	chr6:71379400-71386400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:71379400-71388400	Weak transcription	Right Ventricle	heart
28	chr6:71379400-71394600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:71379600-71383200	Weak transcription	NHEK	skin
30	chr6:71379600-71388200	Weak transcription	Primary B cells from cord blood	blood
31	chr6:71379800-71383000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:71380000-71382800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:71380000-71382800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:71380000-71385000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:71380200-71383000	Weak transcription	HUVEC	blood vessel
36	chr6:71380200-71396200	Weak transcription	Brain Angular Gyrus	brain
37	chr6:71380400-71383600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:71381000-71393800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:71381200-71383000	Weak transcription	Fetal Stomach	stomach
40	chr6:71381400-71383000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr6:71381600-71382800	Enhancers	Primary T cells from cord blood	blood
42	chr6:71381600-71383400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr6:71381600-71386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:71381800-71382800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr6:71381800-71382800	Enhancers	Stomach Mucosa	stomach
46	chr6:71381800-71383000	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:71381800-71383400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr6:71381800-71384200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr6:71382000-71383000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:71382000-71383000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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