Variant report

Variant	rs7002369
Chromosome Location	chr8:61168775-61168776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61167771..61170753-chr8:61173259..61175259,2	K562	blood:
2	chr8:61168507..61170883-chr8:61192762..61195165,2	MCF-7	breast:
3	chr8:61163880..61166402-chr8:61167523..61169241,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178538	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10086200	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10086341	0.84[AFR][1000 genomes]
rs10086352	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10086449	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10093008	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10094224	0.82[CEU][hapmap]
rs10094523	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10097537	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101374	0.83[AFR][1000 genomes]
rs10109265	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10109487	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10435600	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10957125	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11774698	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11774872	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778498	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11781514	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11994317	0.88[AFR][1000 genomes]
rs13266513	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13267008	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13269899	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13269948	0.88[AFR][1000 genomes]
rs13272076	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs13274525	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13280153	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13281067	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28371059	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28376554	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28429093	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28481384	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28532174	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28759336	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35552143	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4737556	0.88[AFR][1000 genomes]
rs6471851	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471852	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471853	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471855	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471856	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471859	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6471860	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6983247	0.82[CEU][hapmap]
rs6983830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987786	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6988169	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6990370	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6998446	0.92[ASW][hapmap];0.96[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs6998745	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7002077	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7002846	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs7002871	0.84[AFR][1000 genomes]
rs7003287	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7004004	0.91[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7006734	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7007157	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7009243	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7009482	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7463930	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463939	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7464181	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7464531	0.83[AFR][1000 genomes]
rs7812953	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7813357	0.84[AFR][1000 genomes]
rs7814280	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7814473	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7825247	0.87[AFR][1000 genomes]
rs7826329	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7832414	0.82[CEU][hapmap]
rs7832419	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7840279	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841372	0.89[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7841396	0.81[AFR][1000 genomes]
rs7841804	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7843385	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7845524	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180936	0.87[YRI][hapmap]
rs9643367	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9643368	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1022752	chr8:61095248-61322302	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv831333	chr8:61102862-61275122	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv3371465	chr8:61115030-61356658	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv890943	chr8:61134995-61225652	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831334	chr8:61148796-61330190	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7002369	PALM3	trans	cerebellum	SCAN
rs7002369	CA8	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61158600-61174600	Weak transcription	Fetal Intestine Large	intestine
2	chr8:61158800-61176800	Weak transcription	A549	lung
3	chr8:61162000-61170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:61164000-61171800	Strong transcription	K562	blood
5	chr8:61164200-61186600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr8:61164600-61169400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:61166000-61169000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr8:61167000-61177400	Weak transcription	Fetal Thymus	thymus
9	chr8:61167000-61180200	Weak transcription	Left Ventricle	heart
10	chr8:61167000-61193200	Weak transcription	Gastric	stomach
11	chr8:61167000-61193200	Weak transcription	Lung	lung
12	chr8:61167000-61193200	Weak transcription	Pancreas	Pancrea
13	chr8:61167200-61174600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:61167600-61172200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr8:61167600-61186400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr8:61167800-61175600	Weak transcription	Fetal Intestine Small	intestine
17	chr8:61168200-61170400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr8:61168200-61176800	Weak transcription	Fetal Stomach	stomach

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