Variant report

Variant	rs13278798
Chromosome Location	chr8:103344832-103344833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103335858..103340204-chr8:103341217..103345311,4	MCF-7	breast:
2	chr8:103342144..103347475-chr8:103421612..103426847,6	MCF-7	breast:
3	chr8:103342633..103344961-chr8:103423576..103425389,2	MCF-7	breast:
4	chr8:103343757..103347850-chr8:103350455..103353849,3	MCF-7	breast:
5	chr8:103343558..103345288-chr8:103423170..103425370,2	K562	blood:

Variant related genes	Relation type
ENSG00000104517	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10090707	1.00[MEX][hapmap]
rs10505020	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10955286	1.00[ASN][1000 genomes]
rs10955287	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11369820	1.00[ASN][1000 genomes]
rs12707772	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs13248603	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13249355	1.00[ASN][1000 genomes]
rs13249865	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13250998	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13259151	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13261528	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13262662	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13262857	1.00[ASN][1000 genomes]
rs13263132	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13268883	1.00[ASN][1000 genomes]
rs13269273	0.80[CEU][hapmap]
rs13269311	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13270908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13271493	1.00[ASN][1000 genomes]
rs13278875	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2061299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs28927991	0.90[EUR][1000 genomes]
rs28999669	0.89[EUR][1000 genomes]
rs34078231	1.00[ASN][1000 genomes]
rs34270914	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34278087	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34279135	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34297513	0.92[EUR][1000 genomes]
rs34351006	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34356268	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34676997	1.00[ASN][1000 genomes]
rs34730203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913297	1.00[ASN][1000 genomes]
rs34976508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35166521	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35316247	0.93[EUR][1000 genomes]
rs35558370	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35655607	1.00[ASN][1000 genomes]
rs35873559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35969173	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35980679	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36178006	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4483125	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55804830	1.00[ASN][1000 genomes]
rs56003023	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59572423	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71506353	1.00[ASN][1000 genomes]
rs71518852	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71518861	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71518862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71518868	1.00[ASN][1000 genomes]
rs7845877	0.88[EUR][1000 genomes]
rs9650000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9650001	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9650002	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers 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	19 gene(s)	inside rSNPs	diseases
7	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv528486	chr8:103279922-103373304	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv891244	chr8:103309862-103483466	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv831412	chr8:103337196-103536397	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13278798	KCNS2	cis	parietal	SCAN
rs13278798	RIMS2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103325600-103358200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr8:103326000-103354000	Weak transcription	Lung	lung
3	chr8:103330000-103346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr8:103330000-103375200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:103335000-103345400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:103335200-103345400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr8:103335400-103345000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr8:103335400-103345000	Strong transcription	Fetal Muscle Leg	muscle
9	chr8:103335400-103345200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:103335400-103345200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr8:103335400-103345200	Strong transcription	Adipose Nuclei	Adipose
12	chr8:103335400-103345200	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr8:103335400-103345400	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr8:103335400-103345400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:103335400-103346400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr8:103335400-103346600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr8:103335400-103346600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr8:103335400-103347000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr8:103335400-103351200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr8:103335400-103355000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr8:103335400-103360000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr8:103335400-103361200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr8:103335400-103361400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr8:103335400-103363400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr8:103335400-103363800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr8:103335400-103373200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr8:103335400-103373400	Strong transcription	Fetal Thymus	thymus
28	chr8:103335400-103373600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr8:103335800-103355800	Strong transcription	GM12878-XiMat	blood
30	chr8:103335800-103370200	Strong transcription	Dnd41	blood
31	chr8:103336000-103352200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:103336400-103353200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr8:103337000-103345200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr8:103337000-103380000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr8:103337800-103346400	Strong transcription	Primary hematopoietic stem cells	blood
36	chr8:103338400-103345400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr8:103338400-103345400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr8:103339400-103359000	Weak transcription	Spleen	Spleen
39	chr8:103339600-103345200	Strong transcription	Fetal Kidney	kidney
40	chr8:103339600-103354000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr8:103339600-103359000	Weak transcription	Colonic Mucosa	Colon
42	chr8:103340600-103345200	Weak transcription	Brain Substantia Nigra	brain
43	chr8:103340600-103349200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr8:103340800-103354000	Weak transcription	Right Ventricle	heart
45	chr8:103340800-103357600	Weak transcription	HSMMtube	muscle
46	chr8:103340800-103379400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr8:103341200-103346000	Strong transcription	Primary B cells from cord blood	blood
48	chr8:103341200-103346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr8:103341400-103346600	Weak transcription	Fetal Stomach	stomach
50	chr8:103341400-103354000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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