Variant report

Variant	rs1043290
Chromosome Location	chr2:37072266-37072267
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37070373..37072769-chr2:37080148..37082605,2	K562	blood:
2	chr2:37070518..37072329-chr2:37074111..37076172,2	K562	blood:
3	chr2:37068151..37070389-chr2:37071740..37074179,2	K562	blood:
4	chr2:37070468..37072403-chr2:37075217..37077956,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STRN-1	chr2:37071730-37073048	NONHSAT070091

Variant related genes	Relation type
ENSG00000268688	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1015600	0.98[ASN][1000 genomes]
rs10164948	0.80[EUR][1000 genomes]
rs10166161	0.80[EUR][1000 genomes]
rs10176081	0.80[EUR][1000 genomes]
rs10176124	0.80[EUR][1000 genomes]
rs10180003	0.80[EUR][1000 genomes]
rs10182741	0.88[EUR][1000 genomes]
rs10183626	0.81[EUR][1000 genomes]
rs10185737	0.88[EUR][1000 genomes]
rs10189328	1.00[EUR][1000 genomes]
rs10189918	0.88[EUR][1000 genomes]
rs10201963	0.88[EUR][1000 genomes]
rs10202311	0.88[EUR][1000 genomes]
rs11124549	0.94[ASN][1000 genomes]
rs11673811	0.80[EUR][1000 genomes]
rs11678807	0.80[EUR][1000 genomes]
rs11680617	0.80[EUR][1000 genomes]
rs11680663	0.80[EUR][1000 genomes]
rs11682966	0.82[ASN][1000 genomes]
rs11685600	0.88[EUR][1000 genomes]
rs12479195	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12624290	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13020894	0.85[ASN][1000 genomes]
rs13388406	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13401327	0.92[EUR][1000 genomes]
rs13408941	1.00[EUR][1000 genomes]
rs13413438	0.88[EUR][1000 genomes]
rs13432707	0.80[EUR][1000 genomes]
rs17020005	0.84[ASN][1000 genomes]
rs17020024	0.82[ASN][1000 genomes]
rs17020084	0.88[EUR][1000 genomes]
rs17442690	0.93[ASN][1000 genomes]
rs17442739	0.93[ASN][1000 genomes]
rs1861433	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1861434	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1861436	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2041828	0.81[EUR][1000 genomes]
rs2160379	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2216106	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2255330	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287087	0.93[ASN][1000 genomes]
rs2302658	0.96[EUR][1000 genomes]
rs2372812	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2540918	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2540919	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2540920	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2540925	0.84[ASN][1000 genomes]
rs2540931	0.84[ASN][1000 genomes]
rs2540936	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2540939	0.94[ASN][1000 genomes]
rs2540940	0.93[ASN][1000 genomes]
rs2540941	0.94[ASN][1000 genomes]
rs2691104	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2691109	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691110	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691114	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2691115	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2691116	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2691118	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2717492	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2717494	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2717495	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2717496	0.82[ASN][1000 genomes]
rs2717501	0.85[ASN][1000 genomes]
rs2717505	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2717508	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2717509	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2717510	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2717511	0.98[ASN][1000 genomes]
rs2717512	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2717516	0.81[AMR][1000 genomes]
rs2717518	0.82[ASN][1000 genomes]
rs2717519	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2717520	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2717522	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28718824	0.96[EUR][1000 genomes]
rs28754306	0.96[EUR][1000 genomes]
rs2888418	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35622893	0.81[EUR][1000 genomes]
rs41486347	0.84[ASN][1000 genomes]
rs6715033	0.84[ASN][1000 genomes]
rs6739553	0.82[ASN][1000 genomes]
rs6756876	0.84[ASN][1000 genomes]
rs6759472	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs723673	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7562109	0.92[EUR][1000 genomes]
rs7579735	0.96[EUR][1000 genomes]
rs9789527	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9789649	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs998321	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][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	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1011014	chr2:37027819-37095895	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv999465	chr2:37029347-37095895	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37062400-37074000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr2:37062400-37075800	Weak transcription	Brain Germinal Matrix	brain
3	chr2:37062800-37073800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:37062800-37076000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:37062800-37095600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:37063000-37074000	Weak transcription	Dnd41	blood
7	chr2:37063000-37074200	Weak transcription	Primary T cells from cord blood	blood
8	chr2:37063000-37076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:37063000-37093600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:37063200-37074200	Weak transcription	HUVEC	blood vessel
11	chr2:37064000-37076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:37065800-37074000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:37065800-37104200	Weak transcription	Right Ventricle	heart
14	chr2:37066000-37076200	Weak transcription	Lung	lung
15	chr2:37066200-37075200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:37066400-37076200	Weak transcription	Fetal Stomach	stomach
17	chr2:37066800-37076200	Weak transcription	Brain Substantia Nigra	brain
18	chr2:37066800-37092800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:37067400-37076000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:37067400-37076400	Weak transcription	Aorta	Aorta
21	chr2:37067400-37083800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:37067400-37103200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:37067600-37074000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:37067600-37074000	Weak transcription	Left Ventricle	heart
25	chr2:37067600-37074000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:37067600-37074200	Weak transcription	Adipose Nuclei	Adipose
27	chr2:37067600-37074200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:37067600-37075200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:37067600-37075200	Weak transcription	Fetal Intestine Large	intestine
30	chr2:37067600-37075200	Weak transcription	Ovary	ovary
31	chr2:37067600-37076200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:37067600-37076400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:37067600-37083800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:37067600-37103000	Weak transcription	Small Intestine	intestine
35	chr2:37067600-37146200	Weak transcription	Psoas Muscle	Psoas
36	chr2:37067800-37074000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr2:37068000-37074000	Weak transcription	Brain Anterior Caudate	brain
38	chr2:37068000-37074200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:37068200-37074000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:37068200-37074000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:37068200-37074000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:37068200-37075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:37068200-37075200	Weak transcription	Fetal Muscle Leg	muscle
44	chr2:37068200-37075800	Weak transcription	NH-A	brain
45	chr2:37068400-37074600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:37068400-37074800	Weak transcription	Placenta	Placenta
47	chr2:37068400-37076200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:37068400-37076200	Weak transcription	HMEC	breast
49	chr2:37068400-37095600	Weak transcription	Fetal Kidney	kidney
50	chr2:37068600-37074000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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