Variant report

Variant	rs1030901
Chromosome Location	chr2:101007314-101007315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:101005691..101009453-chr2:101017314..101020656,3	MCF-7	breast:
2	chr2:101007069..101008727-chr2:101012346..101015344,2	MCF-7	breast:
3	chr2:101003802..101007409-chr2:101009327..101011119,3	K562	blood:
4	chr2:100889322..100890930-chr2:101005825..101008578,2	K562	blood:
5	chr2:100999492..101001817-chr2:101006206..101007709,2	MCF-7	breast:

Extended variants
information (count: 156 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10048665	0.89[EUR][1000 genomes]
rs10174145	0.91[EUR][1000 genomes]
rs10180423	0.93[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10182399	0.90[EUR][1000 genomes]
rs10183150	0.87[EUR][1000 genomes]
rs10186134	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10193204	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10194210	0.83[EUR][1000 genomes]
rs10195793	0.84[EUR][1000 genomes]
rs10202326	0.92[EUR][1000 genomes]
rs1030902	0.96[EUR][1000 genomes]
rs10460478	0.85[EUR][1000 genomes]
rs11123824	0.84[EUR][1000 genomes]
rs11123826	0.88[CEU][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs11123827	0.89[EUR][1000 genomes]
rs1114595	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11674569	0.96[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11674830	0.93[EUR][1000 genomes]
rs11675901	0.91[EUR][1000 genomes]
rs11678148	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11678158	0.91[EUR][1000 genomes]
rs11680660	0.91[EUR][1000 genomes]
rs11682557	0.91[EUR][1000 genomes]
rs11682748	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs11683088	0.84[EUR][1000 genomes]
rs11683121	0.85[EUR][1000 genomes]
rs11684004	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11684516	0.93[EUR][1000 genomes]
rs11685250	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs11685406	0.92[EUR][1000 genomes]
rs11686293	0.84[EUR][1000 genomes]
rs11686649	0.92[EUR][1000 genomes]
rs11686799	0.92[EUR][1000 genomes]
rs11686842	0.92[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs11686880	0.92[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11687352	0.85[EUR][1000 genomes]
rs11687865	0.86[EUR][1000 genomes]
rs11688285	0.91[EUR][1000 genomes]
rs11689439	0.83[EUR][1000 genomes]
rs11691135	0.81[CEU][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs11691684	0.87[EUR][1000 genomes]
rs11693044	0.84[EUR][1000 genomes]
rs11693424	0.83[EUR][1000 genomes]
rs11693471	0.91[EUR][1000 genomes]
rs11694642	0.92[EUR][1000 genomes]
rs11694700	0.91[EUR][1000 genomes]
rs11892034	0.91[EUR][1000 genomes]
rs11895772	0.82[EUR][1000 genomes]
rs12373827	0.89[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs12615466	0.84[EUR][1000 genomes]
rs12617779	0.91[EUR][1000 genomes]
rs12618908	0.91[EUR][1000 genomes]
rs12621892	0.91[EUR][1000 genomes]
rs12622318	0.84[EUR][1000 genomes]
rs12712075	0.84[EUR][1000 genomes]
rs12989897	0.91[EUR][1000 genomes]
rs12990688	0.82[EUR][1000 genomes]
rs12991172	0.91[EUR][1000 genomes]
rs12991577	0.94[EUR][1000 genomes]
rs12997725	0.90[EUR][1000 genomes]
rs12999151	0.91[EUR][1000 genomes]
rs12999779	0.84[EUR][1000 genomes]
rs13001423	0.83[EUR][1000 genomes]
rs13006224	0.83[EUR][1000 genomes]
rs13020451	0.84[EUR][1000 genomes]
rs13021801	0.89[EUR][1000 genomes]
rs13023534	0.83[EUR][1000 genomes]
rs13026570	0.91[EUR][1000 genomes]
rs13031711	0.91[EUR][1000 genomes]
rs13031906	0.91[EUR][1000 genomes]
rs1437967	0.92[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1437969	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1530028	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1530029	0.94[EUR][1000 genomes]
rs1530030	0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs1530031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1811415	0.93[EUR][1000 genomes]
rs1837143	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1866198	0.84[EUR][1000 genomes]
rs1946799	0.81[EUR][1000 genomes]
rs1967339	0.83[EUR][1000 genomes]
rs1967341	0.84[EUR][1000 genomes]
rs2099611	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];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164847	0.92[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2241809	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs2241810	0.96[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2241811	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2309798	0.92[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2309800	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2309852	0.94[EUR][1000 genomes]
rs3748930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3828193	0.88[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4149505	0.93[EUR][1000 genomes]
rs4149507	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs4149510	0.88[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4149512	0.88[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4149513	0.88[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4149517	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4149518	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs4149523	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264577	0.88[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs4340543	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4378827	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4387816	0.94[EUR][1000 genomes]
rs4407265	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477940	0.92[EUR][1000 genomes]
rs4635546	0.84[EUR][1000 genomes]
rs4640404	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4850927	0.85[CEU][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4850929	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4850930	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4850931	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851288	0.93[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs4851292	0.84[EUR][1000 genomes]
rs4851293	0.84[EUR][1000 genomes]
rs4851294	0.92[EUR][1000 genomes]
rs4851297	0.89[EUR][1000 genomes]
rs4851298	0.91[EUR][1000 genomes]
rs4851302	0.91[EUR][1000 genomes]
rs4851303	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851304	0.93[EUR][1000 genomes]
rs4851305	0.89[EUR][1000 genomes]
rs4851310	0.94[EUR][1000 genomes]
rs4851311	0.94[EUR][1000 genomes]
rs4851312	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851313	0.82[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62148360	0.95[EUR][1000 genomes]
rs6542940	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6542942	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542944	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542947	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716636	0.92[CEU][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs6725052	0.91[EUR][1000 genomes]
rs6731549	0.92[CEU][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs6736311	0.92[EUR][1000 genomes]
rs6737217	0.96[EUR][1000 genomes]
rs6749018	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6754176	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757754	0.92[EUR][1000 genomes]
rs74177694	0.92[EUR][1000 genomes]
rs74177695	0.87[EUR][1000 genomes]
rs74177696	0.85[EUR][1000 genomes]
rs7425449	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7425797	0.84[EUR][1000 genomes]
rs7585582	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7590388	0.85[EUR][1000 genomes]
rs7597615	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs893416	0.90[EUR][1000 genomes]
rs920269	0.84[EUR][1000 genomes]
rs920270	0.85[EUR][1000 genomes]
rs930374	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9973536	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1030901	LONRF2	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100993200-101017800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:100996400-101007600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:100997800-101008400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:100998200-101008400	Weak transcription	Dnd41	blood
5	chr2:100998200-101008800	Weak transcription	GM12878-XiMat	blood
6	chr2:100998200-101009000	Weak transcription	A549	lung
7	chr2:100998200-101022600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:100998400-101010000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:101000400-101009400	Weak transcription	HepG2	liver
10	chr2:101002000-101008200	Weak transcription	Right Ventricle	heart
11	chr2:101002000-101009000	Weak transcription	Gastric	stomach
12	chr2:101002000-101023400	Weak transcription	Psoas Muscle	Psoas
13	chr2:101002200-101007800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:101002400-101007400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:101002400-101008400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:101002400-101012000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:101003200-101021000	Weak transcription	K562	blood
18	chr2:101003400-101008200	Weak transcription	Lung	lung
19	chr2:101003600-101007600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:101003800-101007400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:101005000-101008200	Weak transcription	Aorta	Aorta
22	chr2:101005200-101007400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:101005200-101007800	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:101005200-101008000	Weak transcription	Fetal Lung	lung
25	chr2:101005200-101008200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:101005200-101008200	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:101005200-101015000	Strong transcription	Fetal Brain Female	brain
28	chr2:101005400-101008200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:101005400-101008200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:101005600-101007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:101005600-101008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:101005600-101008200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:101005600-101008600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:101005600-101017600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:101005600-101032800	Weak transcription	HUVEC	blood vessel
36	chr2:101005800-101007600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:101005800-101007600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:101005800-101007600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:101005800-101007600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:101005800-101033000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:101006000-101007600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:101006000-101007600	Weak transcription	Adipose Nuclei	Adipose
43	chr2:101006000-101007600	Weak transcription	Fetal Intestine Small	intestine
44	chr2:101006000-101007600	Weak transcription	Left Ventricle	heart
45	chr2:101006000-101007600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:101006000-101007600	Weak transcription	Thymus	Thymus
47	chr2:101006000-101008200	Weak transcription	Fetal Thymus	thymus
48	chr2:101006000-101008600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:101006000-101009200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:101006000-101021600	Weak transcription	Colon Smooth Muscle	Colon

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