Variant report

Variant	rs929916
Chromosome Location	chr2:86305814-86305815
allele	C/T
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	chr2:86054004..86055894-chr2:86304722..86306644,12	MCF-7	breast:
2	chr2:85956028..85956647-chr2:86305693..86306484,2	MCF-7	breast:
3	chr2:86054589..86055163-chr2:86305452..86306492,4	K562	blood:
4	chr2:86303491..86306456-chr2:86374651..86377293,2	K562	blood:
5	chr2:86301883..86303571-chr2:86305517..86307251,2	K562	blood:
6	chr2:86299304..86302856-chr2:86304036..86307072,4	MCF-7	breast:
7	chr2:86054177..86056826-chr2:86305154..86307872,2	MCF-7	breast:
8	chr2:86278837..86281699-chr2:86305012..86307406,2	K562	blood:
9	chr2:86252439..86253030-chr2:86305581..86306554,3	MCF-7	breast:

No data

Extended variants
information (count: 89 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10187875	1.00[ASN][1000 genomes]
rs10191567	0.87[TSI][hapmap]
rs10779967	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11127015	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11127018	0.88[MEX][hapmap]
rs11885520	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11886175	1.00[ASN][1000 genomes]
rs11890563	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891096	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895453	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12473739	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][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	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431245	0.92[ASN][1000 genomes]
rs1424516	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1424520	0.83[GIH][hapmap]
rs1469982	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1559513	1.00[JPT][hapmap]
rs2059353	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2288117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288121	0.83[GIH][hapmap]
rs311561	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311565	0.85[CEU][hapmap]
rs311567	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs311569	0.85[CEU][hapmap]
rs311570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311571	0.85[CEU][hapmap]
rs311572	0.85[CEU][hapmap]
rs311573	0.85[CEU][hapmap]
rs311580	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311582	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311583	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311584	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892520	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770073	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810828	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4832027	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs4832028	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4832239	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4832250	0.83[GIH][hapmap]
rs4832254	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][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	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6547666	1.00[JPT][hapmap]
rs6707736	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6715623	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6720431	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][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	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72847853	1.00[ASN][1000 genomes]
rs7340327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419344	1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7558040	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][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[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs889911	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs918856	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9677675	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9679308	1.00[ASN][1000 genomes]
rs979940	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs929916	POLR1A	cis	lymphoblastoid	seeQTL
rs929916	MRPL35	cis	Esophagus Muscularis	GTEx
rs929916	MRPL35	cis	Artery Aorta	GTEx
rs929916	POLR1A	cis	Nerve Tibial	GTEx
rs929916	MRPL35	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:86286200-86310400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:86286200-86311200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:86289800-86307200	Strong transcription	HepG2	liver
9	chr2:86290200-86310800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:86290600-86306200	Strong transcription	Fetal Intestine Large	intestine
11	chr2:86290800-86310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:86290800-86314600	Strong transcription	HMEC	breast
13	chr2:86290800-86318600	Strong transcription	K562	blood
14	chr2:86290800-86322600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr2:86291000-86311200	Strong transcription	Fetal Brain Female	brain
16	chr2:86291600-86319000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:86291800-86311400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:86291800-86318800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:86292800-86331000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:86294800-86309600	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr2:86295200-86323200	Strong transcription	Fetal Stomach	stomach
22	chr2:86295600-86306600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr2:86295800-86308400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:86295800-86308600	Strong transcription	Brain Germinal Matrix	brain
25	chr2:86295800-86308600	Strong transcription	NHEK	skin
26	chr2:86296000-86322400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:86296200-86306400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:86296400-86306000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:86296400-86306000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:86296400-86307600	Weak transcription	Fetal Heart	heart
31	chr2:86296600-86307200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:86296800-86306400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:86297200-86307000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:86297400-86307400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:86297600-86306400	Strong transcription	Dnd41	blood
36	chr2:86298600-86307400	Weak transcription	Fetal Brain Male	brain
37	chr2:86299000-86306600	Strong transcription	Fetal Intestine Small	intestine
38	chr2:86299200-86310400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:86299400-86308000	Genic enhancers	Fetal Thymus	thymus
40	chr2:86299400-86308200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:86299800-86306200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:86299800-86306800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:86299800-86308000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:86300000-86307000	Strong transcription	NHLF	lung
45	chr2:86300000-86318200	Strong transcription	Placenta	Placenta
46	chr2:86300000-86323000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:86300000-86331800	Weak transcription	Stomach Mucosa	stomach
48	chr2:86300200-86306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:86300200-86306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:86300400-86307000	Strong transcription	Stomach Smooth Muscle	stomach

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