Variant report

Variant	rs7843385
Chromosome Location	chr8:61187018-61187019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:61184957..61187157-chr8:61191809..61194073,2	MCF-7	breast:
2	chr8:61185501..61190567-chr8:61191860..61196819,8	MCF-7	breast:
3	chr8:61181860..61184395-chr8:61185905..61188590,3	MCF-7	breast:
4	chr8:61185497..61188035-chr8:61257935..61259723,3	K562	blood:

Variant related genes	Relation type
ENSG00000178538	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10086200	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10086352	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10086449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10089297	0.81[EUR][1000 genomes]
rs10093008	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10094224	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs10094523	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10097537	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10097613	0.81[EUR][1000 genomes]
rs10098038	0.81[EUR][1000 genomes]
rs10105098	0.81[EUR][1000 genomes]
rs10105158	0.81[EUR][1000 genomes]
rs10109265	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10109487	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10112099	0.81[EUR][1000 genomes]
rs10112677	0.81[EUR][1000 genomes]
rs10435600	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10957125	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11774698	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11774872	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11778498	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11781514	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13266513	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13267008	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13269899	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13274525	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13280153	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13280906	0.81[EUR][1000 genomes]
rs13281067	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13281126	0.81[EUR][1000 genomes]
rs1480341	0.81[EUR][1000 genomes]
rs28371059	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376554	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429093	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28481384	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532174	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28759336	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35256935	0.81[EUR][1000 genomes]
rs35503542	0.81[EUR][1000 genomes]
rs35552143	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4351453	0.81[EUR][1000 genomes]
rs4584176	0.81[EUR][1000 genomes]
rs6471851	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471852	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471853	0.80[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs6471855	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471856	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471857	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471858	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471859	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6983247	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs6983830	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6987786	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6988169	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6990370	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6998745	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7002077	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7002369	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]
rs7003287	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7006734	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7007157	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7009243	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7009482	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7463930	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7463939	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7464181	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7465560	0.81[EUR][1000 genomes]
rs7812953	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7814280	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7814473	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7826329	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7832414	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs7832419	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7840279	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7841372	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841458	0.81[EUR][1000 genomes]
rs7841804	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845524	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9298028	0.81[EUR][1000 genomes]
rs9298031	0.81[EUR][1000 genomes]
rs9298032	0.81[EUR][1000 genomes]
rs9298033	0.81[EUR][1000 genomes]
rs9643367	0.80[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9643368	0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9657070	0.80[EUR][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
rs7843385	PALM3	trans	cerebellum	SCAN
rs7843385	CA8	cis	lung	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61167000-61193200	Weak transcription	Gastric	stomach
2	chr8:61167000-61193200	Weak transcription	Lung	lung
3	chr8:61167000-61193200	Weak transcription	Pancreas	Pancrea
4	chr8:61172800-61191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:61173000-61187600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr8:61178000-61191000	Weak transcription	Fetal Stomach	stomach
7	chr8:61179800-61191000	Weak transcription	Fetal Intestine Small	intestine
8	chr8:61184800-61187400	Enhancers	Fetal Thymus	thymus
9	chr8:61184800-61190400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr8:61185200-61189000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr8:61185800-61187800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr8:61186200-61190800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr8:61186400-61187200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr8:61186400-61187200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:61186600-61187200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr8:61186600-61187200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr8:61186600-61187400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr8:61186600-61187400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr8:61186600-61187600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr8:61186600-61187600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr8:61186600-61187600	Transcr. at gene 5' and 3'	K562	blood
22	chr8:61186800-61187800	Flanking Active TSS	A549	lung
23	chr8:61187000-61187200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:61187000-61187200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr8:61187000-61187200	Enhancers	Brain Anterior Caudate	brain
26	chr8:61187000-61189000	Strong transcription	Fetal Intestine Large	intestine

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