Variant report

Variant	rs10779967
Chromosome Location	chr2:86330726-86330727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86329948..86332562-chr2:86408427..86410374,2	MCF-7	breast:
2	chr2:86329235..86331998-chr2:86357573..86360171,2	K562	blood:
3	chr2:86329731..86334667-chr2:86420655..86424478,8	K562	blood:
4	chr2:86330519..86334714-chr2:86420374..86424108,6	K562	blood:

Variant related genes	Relation type
ENSG00000132305	Chromatin interaction
ENSG00000273080	Chromatin interaction
ENSG00000132300	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10187875	1.00[ASN][1000 genomes]
rs10427394	0.87[CEU][hapmap]
rs11127015	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127018	0.88[MEX][hapmap]
rs11885520	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11891096	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11895453	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12473739	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs13353	0.91[ASN][1000 genomes]
rs13390107	1.00[ASN][1000 genomes]
rs13420958	1.00[ASN][1000 genomes]
rs13431245	0.92[ASN][1000 genomes]
rs1424516	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424520	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs1469982	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1559513	1.00[JPT][hapmap]
rs1559516	0.87[CEU][hapmap]
rs2059353	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288117	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2288121	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs311561	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs311567	0.83[GIH][hapmap]
rs311570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs311580	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs311582	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs311583	1.00[ASN][1000 genomes]
rs311584	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34892520	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3770073	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3810828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832027	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4832028	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4832239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832242	0.87[CEU][hapmap]
rs4832250	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs4832254	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs4832258	1.00[JPT][hapmap]
rs57339071	1.00[ASN][1000 genomes]
rs58077381	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6547666	1.00[JPT][hapmap]
rs6707736	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6715623	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723248	1.00[ASN][1000 genomes]
rs6725046	0.83[ASW][hapmap]
rs6749218	1.00[ASN][1000 genomes]
rs6752561	1.00[ASN][1000 genomes]
rs6758535	1.00[JPT][hapmap]
rs72847843	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7419344	1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7558040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7565645	1.00[JPT][hapmap]
rs7583021	1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7592211	0.91[ASN][1000 genomes]
rs7597608	0.82[ASN][1000 genomes]
rs7599498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[ASN][1000 genomes]
rs889911	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs918856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929916	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9677675	1.00[ASN][1000 genomes]
rs9679308	1.00[ASN][1000 genomes]
rs979940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv582371	chr2:86296566-86507688	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
18	nsv531381	chr2:86301091-86478346	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv1001157	chr2:86301440-86508168	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10779967	POLR1A	cis	Nerve Tibial	GTEx
rs10779967	POLR1A	cis	lymphoblastoid	seeQTL
rs10779967	MRPL35	Cis_1M	lymphoblastoid	RTeQTL
rs10779967	MRPL35	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:86292800-86331000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:86300000-86331800	Weak transcription	Stomach Mucosa	stomach
7	chr2:86307800-86331000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:86308000-86330800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:86312000-86331400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:86312400-86331400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:86314000-86330800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:86317200-86332200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:86319400-86330800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:86319400-86331000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:86320600-86331400	Strong transcription	Primary B cells from cord blood	blood
16	chr2:86320800-86331000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:86320800-86331200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:86321200-86331400	Weak transcription	Fetal Brain Male	brain
19	chr2:86322400-86330800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:86322400-86330800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:86322400-86332400	Weak transcription	Gastric	stomach
22	chr2:86322600-86332000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:86323400-86330800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr2:86323400-86331000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:86323600-86330800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:86323600-86331200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:86324200-86330800	Strong transcription	Fetal Thymus	thymus
28	chr2:86324200-86331000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:86324400-86330800	Strong transcription	HUVEC	blood vessel
30	chr2:86324600-86330800	Strong transcription	NHEK	skin
31	chr2:86325400-86331200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:86325400-86332000	Weak transcription	Fetal Kidney	kidney
33	chr2:86325600-86330800	Strong transcription	Primary T cells from cord blood	blood
34	chr2:86325600-86331000	Weak transcription	Fetal Heart	heart
35	chr2:86325600-86331000	Strong transcription	Fetal Muscle Leg	muscle
36	chr2:86325800-86331000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:86325800-86331200	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:86326800-86331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:86327000-86331800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:86327000-86331800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:86327200-86330800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:86327200-86330800	Weak transcription	Right Ventricle	heart
43	chr2:86327200-86331000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:86327200-86331200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:86327200-86331200	Weak transcription	Brain Anterior Caudate	brain
46	chr2:86327200-86332000	Weak transcription	Ovary	ovary
47	chr2:86327200-86332000	Weak transcription	Thymus	Thymus
48	chr2:86327200-86332200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:86327200-86332200	Weak transcription	Aorta	Aorta
50	chr2:86327200-86332200	Weak transcription	Left Ventricle	heart

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