Variant report

Variant	rs1468664
Chromosome Location	chr2:37867494-37867495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37866118..37867665-chr2:37869743..37872565,2	MCF-7	breast:
2	chr2:37859378..37862018-chr2:37863759..37867582,3	K562	blood:
3	chr2:37860354..37862423-chr2:37867033..37868574,2	MCF-7	breast:
4	chr2:37865948..37868247-chr2:37870789..37872523,2	K562	blood:
5	chr2:37860309..37862165-chr2:37866082..37868468,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-QPCT-3	chr2:37832379-37870742	NONHSAT070127

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1013291	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1013292	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12622958	0.83[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs13387842	0.88[ASN][1000 genomes]
rs13392288	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13406302	0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13417833	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13417957	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1468663	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17021174	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2041508	0.89[ASN][1000 genomes]
rs2072419	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2079998	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2098198	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109821	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109822	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159726	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2191841	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373290	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2373292	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3731852	0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3731854	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4372883	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4594425	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4670210	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4670748	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6544095	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs6711909	0.91[CHB][hapmap]
rs6740127	0.83[ASN][1000 genomes]
rs6752119	0.91[CHB][hapmap]
rs6752220	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6752762	0.89[ASN][1000 genomes]
rs6759224	0.95[JPT][hapmap]
rs7607934	0.86[JPT][hapmap]
rs7735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456374	chr2:37669487-37868214	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv470453	chr2:37669487-37868214	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv581473	chr2:37669487-37868214	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37873200	Weak transcription	Liver	Liver
2	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
3	chr2:37857000-37871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:37857200-37868200	Weak transcription	Psoas Muscle	Psoas
5	chr2:37858000-37868600	Weak transcription	A549	lung
6	chr2:37858400-37867600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:37858800-37871400	Weak transcription	Aorta	Aorta
8	chr2:37859000-37868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:37859200-37868600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:37860000-37871200	Weak transcription	Gastric	stomach
11	chr2:37860200-37868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:37860800-37873000	Weak transcription	Pancreas	Pancrea
13	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:37861000-37868000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:37862000-37869400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:37862200-37870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:37862400-37869200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:37862400-37870200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr2:37862800-37869400	Weak transcription	HUVEC	blood vessel
20	chr2:37863200-37868200	Weak transcription	Right Atrium	heart
21	chr2:37863400-37868000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:37863400-37868200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:37863400-37875000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:37863600-37868200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:37863600-37868200	Weak transcription	HMEC	breast
26	chr2:37863600-37868400	Weak transcription	NHEK	skin
27	chr2:37863600-37868800	Weak transcription	Fetal Brain Female	brain
28	chr2:37863600-37871400	Weak transcription	Lung	lung
29	chr2:37863600-37873000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:37864200-37868200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:37864200-37868200	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:37864200-37868600	Weak transcription	Right Ventricle	heart
33	chr2:37864200-37870200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:37864200-37871200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:37864200-37871200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:37864200-37871400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:37864200-37871400	Weak transcription	Spleen	Spleen
38	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:37864400-37868200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:37864400-37870600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:37864400-37871400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:37864400-37871400	Weak transcription	Adipose Nuclei	Adipose
43	chr2:37864400-37872000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:37864400-37879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr2:37864600-37868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:37864600-37868200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr2:37864600-37868200	Weak transcription	Primary T cells from cord blood	blood
48	chr2:37864600-37870200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:37864600-37871000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:37864800-37868400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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