Variant report

Variant	rs12704976
Chromosome Location	chr7:97843979-97843980
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97843013..97845825-chr7:97853837..97855430,2	MCF-7	breast:
2	chr7:97843965..97846398-chr7:97856911..97858412,2	K562	blood:
3	chr7:97839794..97841701-chr7:97843448..97845628,2	MCF-7	breast:
4	chr7:97842812..97845120-chr7:97865672..97868033,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BHLHA15-1	chr7:97842411-97844754	NONHSAT122177

Variant related genes	Relation type
ENSG00000180535	Chromatin interaction
ENSG00000205356	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10215577	0.82[ASN][1000 genomes]
rs10216274	0.82[ASN][1000 genomes]
rs10230846	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10231625	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs10232153	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs10241172	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10243993	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs10256262	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10261777	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs10270280	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs10276472	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10282336	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs13221415	0.90[ASN][1000 genomes]
rs13221480	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[ASN][1000 genomes]
rs13228463	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13241860	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs1532381	0.86[ASN][1000 genomes]
rs17169317	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs17169328	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs28415802	0.82[ASN][1000 genomes]
rs28681561	0.82[ASN][1000 genomes]
rs3148	1.00[CEU][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34320281	0.82[ASN][1000 genomes]
rs35428901	0.90[ASN][1000 genomes]
rs36081491	0.82[ASN][1000 genomes]
rs3735252	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6465655	0.82[ASN][1000 genomes]
rs6958785	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs73404186	0.82[ASN][1000 genomes]
rs7788997	0.82[ASN][1000 genomes]
rs951987	0.86[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv888761	chr7:97829492-97844578	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv888762	chr7:97829492-97853184	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv888763	chr7:97829492-97866291	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv888764	chr7:97832628-97844578	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv888765	chr7:97834386-97853184	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97823000-97851000	Weak transcription	HSMMtube	muscle
2	chr7:97825200-97851000	Weak transcription	Fetal Lung	lung
3	chr7:97836000-97851000	Weak transcription	NHLF	lung
4	chr7:97836600-97846200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:97836600-97847200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:97836800-97857200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:97837000-97846600	Weak transcription	Dnd41	blood
8	chr7:97839200-97844800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:97839200-97851000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:97839800-97844400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr7:97840200-97846000	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:97840200-97847000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:97840200-97847200	Weak transcription	Brain Anterior Caudate	brain
14	chr7:97840200-97847200	Weak transcription	Brain Substantia Nigra	brain
15	chr7:97840200-97851000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:97840400-97845600	Weak transcription	Small Intestine	intestine
17	chr7:97840400-97847000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr7:97840400-97852800	Weak transcription	Brain Angular Gyrus	brain
19	chr7:97840800-97844800	Weak transcription	Aorta	Aorta
20	chr7:97841000-97847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:97841000-97858600	Weak transcription	Psoas Muscle	Psoas
22	chr7:97841200-97844000	Weak transcription	Fetal Brain Female	brain
23	chr7:97841200-97844800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:97841200-97845000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:97841200-97845000	Weak transcription	Left Ventricle	heart
26	chr7:97841200-97845200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:97841200-97845200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:97841200-97845400	Weak transcription	Ovary	ovary
29	chr7:97841200-97846200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:97841200-97850600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:97841200-97850800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:97841200-97850800	Weak transcription	Osteobl	bone
33	chr7:97841200-97852200	Weak transcription	A549	lung
34	chr7:97841200-97867800	Weak transcription	HUVEC	blood vessel
35	chr7:97841200-97880200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr7:97841400-97844400	Weak transcription	Lung	lung
37	chr7:97841400-97844400	Weak transcription	Right Ventricle	heart
38	chr7:97841400-97844800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:97841400-97844800	Weak transcription	Esophagus	oesophagus
40	chr7:97841400-97845400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr7:97841400-97845400	Weak transcription	Liver	Liver
42	chr7:97841400-97846000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:97841400-97846600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:97841400-97847000	Weak transcription	Primary T cells from cord blood	blood
45	chr7:97841400-97847200	Weak transcription	Primary B cells from cord blood	blood
46	chr7:97841400-97850600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:97841400-97858600	Weak transcription	NH-A	brain
48	chr7:97841400-97866200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr7:97841400-97879400	Weak transcription	Fetal Brain Male	brain
50	chr7:97841400-97880200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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