Variant report

Variant	rs2099611
Chromosome Location	chr2:101021090-101021091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:101016960..101019506-chr2:101020404..101023355,2	K562	blood:
2	chr2:101011844..101014323-chr2:101018753..101021911,3	K562	blood:
3	chr2:101021035..101023406-chr2:101025685..101028332,2	MCF-7	breast:
4	chr2:101019685..101022050-chr2:101032463..101034732,2	K562	blood:
5	chr2:100939189..100940921-chr2:101020436..101022884,2	K562	blood:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction
ENSG00000115526	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10048665	0.85[EUR][1000 genomes]
rs10174145	0.87[EUR][1000 genomes]
rs10180423	0.93[CHB][hapmap];0.91[CHD][hapmap];0.82[EUR][1000 genomes]
rs10182399	0.87[EUR][1000 genomes]
rs10183150	0.92[EUR][1000 genomes]
rs10186134	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10193204	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10195793	0.80[EUR][1000 genomes]
rs10202326	0.86[EUR][1000 genomes]
rs1030901	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030902	0.90[EUR][1000 genomes]
rs10460478	0.81[EUR][1000 genomes]
rs11123824	0.81[EUR][1000 genomes]
rs11123826	0.94[CHD][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs11123827	0.84[EUR][1000 genomes]
rs1114595	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674569	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs11674830	0.90[EUR][1000 genomes]
rs11675901	0.85[EUR][1000 genomes]
rs11678148	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs11678158	0.87[EUR][1000 genomes]
rs11680660	0.87[EUR][1000 genomes]
rs11682557	0.85[EUR][1000 genomes]
rs11682748	0.80[EUR][1000 genomes]
rs11683088	0.87[EUR][1000 genomes]
rs11683121	0.81[EUR][1000 genomes]
rs11684004	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs11684516	0.87[EUR][1000 genomes]
rs11685250	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs11685406	0.86[EUR][1000 genomes]
rs11686293	0.80[EUR][1000 genomes]
rs11686649	0.86[EUR][1000 genomes]
rs11686799	0.86[EUR][1000 genomes]
rs11686842	0.82[CEU][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs11686880	0.82[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11687352	0.81[EUR][1000 genomes]
rs11687865	0.81[EUR][1000 genomes]
rs11688285	0.85[EUR][1000 genomes]
rs11691135	0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs11691684	0.83[EUR][1000 genomes]
rs11693044	0.80[EUR][1000 genomes]
rs11693471	0.85[EUR][1000 genomes]
rs11694642	0.86[EUR][1000 genomes]
rs11694700	0.87[EUR][1000 genomes]
rs11892034	0.87[EUR][1000 genomes]
rs12373827	0.92[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs12615466	0.80[EUR][1000 genomes]
rs12617779	0.87[EUR][1000 genomes]
rs12618908	0.85[EUR][1000 genomes]
rs12621892	0.85[EUR][1000 genomes]
rs12622318	0.80[EUR][1000 genomes]
rs12712075	0.80[EUR][1000 genomes]
rs12989897	0.87[EUR][1000 genomes]
rs12991172	0.87[EUR][1000 genomes]
rs12991577	0.90[EUR][1000 genomes]
rs12997725	0.86[EUR][1000 genomes]
rs12999151	0.87[EUR][1000 genomes]
rs12999779	0.81[EUR][1000 genomes]
rs13020451	0.81[EUR][1000 genomes]
rs13021801	0.86[EUR][1000 genomes]
rs13026570	0.87[EUR][1000 genomes]
rs13031711	0.87[EUR][1000 genomes]
rs13031906	0.87[EUR][1000 genomes]
rs1437967	0.92[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1437969	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1530028	0.80[EUR][1000 genomes]
rs1530029	0.88[EUR][1000 genomes]
rs1530030	0.85[CEU][hapmap];0.84[CHD][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs1530031	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1811415	0.90[EUR][1000 genomes]
rs1837143	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866198	0.80[EUR][1000 genomes]
rs1967341	0.80[EUR][1000 genomes]
rs2164847	0.82[CEU][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2241809	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs2241810	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs2241811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309798	0.82[CEU][hapmap];0.81[CHD][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2309800	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2309852	0.88[EUR][1000 genomes]
rs3748930	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828193	0.85[CEU][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs4149505	0.90[EUR][1000 genomes]
rs4149507	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs4149510	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4149512	0.85[CEU][hapmap];0.81[CHD][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs4149513	0.85[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs4149517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4149518	0.89[CEU][hapmap];0.84[CHD][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs4149523	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4264577	0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs4340543	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4378827	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4387816	0.88[EUR][1000 genomes]
rs4407265	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4477940	0.86[EUR][1000 genomes]
rs4635546	0.81[EUR][1000 genomes]
rs4640404	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4850927	0.81[CEU][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4850929	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4850930	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4850931	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851288	0.93[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs4851292	0.80[EUR][1000 genomes]
rs4851293	0.81[EUR][1000 genomes]
rs4851294	0.88[EUR][1000 genomes]
rs4851297	0.83[EUR][1000 genomes]
rs4851298	0.85[EUR][1000 genomes]
rs4851302	0.86[EUR][1000 genomes]
rs4851303	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4851304	0.87[EUR][1000 genomes]
rs4851305	0.84[EUR][1000 genomes]
rs4851310	0.88[EUR][1000 genomes]
rs4851311	0.88[EUR][1000 genomes]
rs4851312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851313	1.00[ASW][hapmap];0.93[CEU][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62148360	0.89[EUR][1000 genomes]
rs6542940	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6542942	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542944	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542947	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6716636	0.82[CEU][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs6725052	0.87[EUR][1000 genomes]
rs6731549	0.81[CEU][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs6736311	0.86[EUR][1000 genomes]
rs6737217	0.90[EUR][1000 genomes]
rs6749018	0.96[EUR][1000 genomes]
rs6754176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757754	0.86[EUR][1000 genomes]
rs74177694	0.88[EUR][1000 genomes]
rs74177695	0.83[EUR][1000 genomes]
rs74177696	0.82[EUR][1000 genomes]
rs7425449	0.80[EUR][1000 genomes]
rs7425797	0.80[EUR][1000 genomes]
rs7585582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7590388	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7597615	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs893416	0.84[EUR][1000 genomes]
rs920269	0.80[EUR][1000 genomes]
rs920270	0.81[EUR][1000 genomes]
rs930374	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9973536	0.92[EUR][1000 genomes]

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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv874701	chr2:100976139-101023261	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2099611	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100998200-101022600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:101002000-101023400	Weak transcription	Psoas Muscle	Psoas
3	chr2:101005600-101032800	Weak transcription	HUVEC	blood vessel
4	chr2:101005800-101033000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:101006000-101021600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:101006600-101023600	Strong transcription	Brain Germinal Matrix	brain
7	chr2:101006600-101031600	Strong transcription	Fetal Stomach	stomach
8	chr2:101007000-101025000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:101007000-101027200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr2:101007200-101032000	Weak transcription	NHDF-Ad	bronchial
11	chr2:101007400-101021600	Weak transcription	HSMMtube	muscle
12	chr2:101007600-101023400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:101007600-101024200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:101007600-101030600	Weak transcription	NH-A	brain
15	chr2:101007800-101021200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:101007800-101023800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:101007800-101024000	Weak transcription	Liver	Liver
18	chr2:101008000-101033000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:101008400-101025200	Weak transcription	Fetal Brain Male	brain
20	chr2:101009000-101022000	Weak transcription	Esophagus	oesophagus
21	chr2:101009200-101023600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:101009400-101026400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:101010000-101021800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:101010000-101022200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:101010000-101022200	Weak transcription	Fetal Kidney	kidney
26	chr2:101010200-101032800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr2:101010800-101022000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:101011000-101022200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:101012000-101024000	Weak transcription	Fetal Heart	heart
30	chr2:101012400-101021600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:101013000-101021200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:101013200-101030400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:101013200-101033000	Weak transcription	Fetal Intestine Large	intestine
34	chr2:101013800-101021400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:101014400-101033200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:101014800-101032400	Weak transcription	Hela-S3	cervix
37	chr2:101015600-101033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:101015800-101024400	Strong transcription	Fetal Brain Female	brain
39	chr2:101015800-101024400	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:101016000-101023800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:101016200-101021200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:101016400-101023400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr2:101016400-101028000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:101016400-101032600	Weak transcription	HSMM	muscle
45	chr2:101016800-101023600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:101016800-101024800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:101017000-101022200	Weak transcription	Right Atrium	heart
48	chr2:101017000-101032800	Weak transcription	Osteobl	bone
49	chr2:101017200-101024800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:101017400-101023000	Strong transcription	Brain Angular Gyrus	brain

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