Variant report

Variant	rs7247000
Chromosome Location	chr19:36441939-36441940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36440986..36443512-chr19:36443562..36445464,2	MCF-7	breast:
2	chr19:36440192..36442486-chr19:36447008..36448982,2	K562	blood:
3	chr19:36431026..36433086-chr19:36440893..36442397,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRFN3-2	chr19:36440386-36442421	NONHSAT065942

Variant related genes	Relation type
ENSG00000267113	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10221461	0.82[ASN][1000 genomes]
rs10221486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1057265	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11878444	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11878880	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11879537	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11880785	1.00[CEU][hapmap]
rs11880835	0.89[ASN][1000 genomes]
rs11880859	0.89[ASN][1000 genomes]
rs11881157	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11882386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11883234	0.87[ASN][1000 genomes]
rs13382036	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242590	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293756	0.89[ASN][1000 genomes]
rs34933126	0.86[EUR][1000 genomes]
rs55686886	0.89[ASN][1000 genomes]
rs56042927	0.89[ASN][1000 genomes]
rs56132838	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56187901	0.89[ASN][1000 genomes]
rs56230692	0.89[ASN][1000 genomes]
rs56744930	0.86[EUR][1000 genomes]
rs56922307	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57068163	0.95[EUR][1000 genomes]
rs57094555	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57516855	0.81[EUR][1000 genomes]
rs57785375	0.89[ASN][1000 genomes]
rs57962062	1.00[EUR][1000 genomes]
rs58161969	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58456578	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58504183	0.91[EUR][1000 genomes]
rs58551711	0.91[EUR][1000 genomes]
rs58768499	0.86[ASN][1000 genomes]
rs58976020	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59150589	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59151712	0.89[ASN][1000 genomes]
rs59399698	0.81[EUR][1000 genomes]
rs59416903	1.00[EUR][1000 genomes]
rs59478831	0.86[EUR][1000 genomes]
rs59534183	0.81[EUR][1000 genomes]
rs60073802	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60276253	0.89[ASN][1000 genomes]
rs60500471	0.89[ASN][1000 genomes]
rs60892678	0.89[ASN][1000 genomes]
rs60935148	0.91[EUR][1000 genomes]
rs61510077	0.85[ASN][1000 genomes]
rs61660311	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61672461	0.86[EUR][1000 genomes]
rs7245383	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7246259	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7246541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247246	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7247769	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7248253	0.89[ASN][1000 genomes]
rs7248265	0.89[ASN][1000 genomes]
rs7249502	0.89[ASN][1000 genomes]
rs7249567	0.92[CHB][hapmap]
rs7251380	0.89[ASN][1000 genomes]
rs7251422	0.82[ASN][1000 genomes]
rs7252053	0.82[ASN][1000 genomes]
rs7252526	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7252572	0.86[ASN][1000 genomes]
rs7252693	0.89[ASN][1000 genomes]
rs7252839	0.89[ASN][1000 genomes]
rs7253086	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7254298	0.89[ASN][1000 genomes]
rs7254335	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7254905	0.89[ASN][1000 genomes]
rs7254994	0.89[ASN][1000 genomes]
rs7255824	0.89[ASN][1000 genomes]
rs7256280	0.86[EUR][1000 genomes]
rs7256433	0.91[EUR][1000 genomes]
rs7256952	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7257789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7257911	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259892	0.89[ASN][1000 genomes]
rs7260613	0.86[EUR][1000 genomes]
rs73599539	0.95[EUR][1000 genomes]
rs73599540	0.95[EUR][1000 genomes]
rs73599546	0.95[EUR][1000 genomes]
rs73599554	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73599561	0.86[EUR][1000 genomes]
rs73599565	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73599577	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73599586	0.86[EUR][1000 genomes]
rs73599600	0.91[EUR][1000 genomes]
rs73599602	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73928364	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73928368	0.89[ASN][1000 genomes]
rs73928369	0.89[ASN][1000 genomes]
rs8110868	0.95[EUR][1000 genomes]
rs909135	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs909136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36429600-36444200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr19:36430000-36450000	Weak transcription	Right Atrium	heart
3	chr19:36431800-36442800	Weak transcription	Thymus	Thymus
4	chr19:36431800-36443000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:36433600-36444200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:36435600-36444000	Weak transcription	Dnd41	blood
7	chr19:36435800-36444000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:36435800-36444400	Weak transcription	Gastric	stomach
9	chr19:36436000-36444800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:36436200-36449000	Weak transcription	Spleen	Spleen
11	chr19:36436600-36444800	Weak transcription	Lung	lung
12	chr19:36436600-36448200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:36437600-36445600	Weak transcription	Fetal Brain Female	brain
14	chr19:36438800-36443000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:36438800-36443000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:36439000-36443200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:36439000-36443800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:36440000-36442200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr19:36440200-36442200	Enhancers	Primary T cells from cord blood	blood
20	chr19:36440200-36443800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr19:36440400-36443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:36440600-36442200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:36441200-36443000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:36441600-36442400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:36441600-36443000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:36441600-36443000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:36441800-36443200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:36441800-36443400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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