Variant report

Variant	rs848619
Chromosome Location	chr2:36810769-36810770
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:36809008..36811077-chr2:36815075..36817974,3	MCF-7	breast:
2	chr2:36809435..36813840-chr2:36817141..36820574,5	K562	blood:
3	chr2:36810053..36812056-chr2:36823147..36825466,2	K562	blood:

Variant related genes	Relation type
ENSG00000256845	Chromatin interaction
ENSG00000171055	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10175266	0.83[EUR][1000 genomes]
rs10178965	0.85[EUR][1000 genomes]
rs10180760	0.83[CEU][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs10180792	0.83[CEU][hapmap]
rs10189554	0.88[EUR][1000 genomes]
rs10194100	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs10197570	0.87[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs10210291	0.80[EUR][1000 genomes]
rs10469897	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10469898	0.96[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11124519	0.84[EUR][1000 genomes]
rs11686443	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs11691600	1.00[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs11691767	0.82[CEU][hapmap]
rs11693359	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11886145	0.85[ASN][1000 genomes]
rs11899523	0.89[ASN][1000 genomes]
rs12105545	0.96[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs13029475	0.84[EUR][1000 genomes]
rs13385408	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13398345	0.90[EUR][1000 genomes]
rs13406169	0.87[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs13406184	0.87[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs13410783	0.84[EUR][1000 genomes]
rs14291	0.96[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1523786	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1533946	0.87[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1533947	0.82[EUR][1000 genomes]
rs1533948	0.87[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1533949	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs17019087	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs17488036	0.83[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2022211	0.87[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2072533	0.93[EUR][1000 genomes]
rs2072534	0.96[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2072535	0.96[CEU][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2075226	0.96[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2110986	0.92[EUR][1000 genomes]
rs2110987	0.84[EUR][1000 genomes]
rs2160403	0.85[EUR][1000 genomes]
rs2160404	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs2276671	0.92[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs34392255	0.94[EUR][1000 genomes]
rs34425257	0.88[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs3770788	0.95[EUR][1000 genomes]
rs3770793	0.83[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs3770796	0.86[ASN][1000 genomes]
rs3770797	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs3770799	0.83[EUR][1000 genomes]
rs3770809	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs3770811	0.87[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs3770818	0.92[CHB][hapmap]
rs3821150	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs5003670	0.83[CEU][hapmap]
rs55700228	0.91[EUR][1000 genomes]
rs57670037	0.84[EUR][1000 genomes]
rs6728602	0.90[EUR][1000 genomes]
rs7570763	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs848596	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs848597	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs848598	0.94[ASN][1000 genomes]
rs848600	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs848601	0.93[ASN][1000 genomes]
rs848610	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848611	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs848612	0.89[EUR][1000 genomes]
rs848613	0.90[EUR][1000 genomes]
rs848614	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs848616	1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs848622	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs848623	0.96[ASN][1000 genomes]
rs848624	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848627	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs848629	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs848630	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848631	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs848635	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs848636	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848638	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848639	0.96[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848640	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs861919	0.83[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9917316	0.92[EUR][1000 genomes]
rs9917318	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs848619	SLC8A1	cis	cerebellum	SCAN
rs848619	CRIM1	cis	cerebellum	SCAN
rs848619	FEZ2	cis	Cerebellum	GTEx
rs848619	FEZ2	cis	parietal	SCAN
rs848619	FEZ2	cis	cerebellum	SCAN
rs848619	FEZ2	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36751000-36824200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:36773000-36811200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:36790200-36818000	Strong transcription	Fetal Intestine Large	intestine
4	chr2:36790800-36812000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:36792200-36824200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:36792800-36811400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:36793200-36811200	Weak transcription	Pancreas	Pancrea
8	chr2:36793200-36816600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:36796000-36818000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:36796800-36818200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:36797000-36814200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:36797800-36813400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:36798000-36818200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:36798200-36818000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:36798400-36818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:36798800-36811200	Weak transcription	Gastric	stomach
17	chr2:36799200-36812800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:36799200-36817400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:36799200-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:36799200-36818200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:36799200-36819200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:36799200-36822600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:36799400-36812800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:36799800-36818000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:36800200-36814400	Strong transcription	Primary hematopoietic stem cells	blood
26	chr2:36800200-36817600	Strong transcription	Liver	Liver
27	chr2:36801000-36817800	Strong transcription	HUVEC	blood vessel
28	chr2:36801200-36810800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:36801400-36813200	Strong transcription	Fetal Lung	lung
30	chr2:36801600-36818000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:36801600-36818000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:36801800-36811200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:36801800-36812200	Strong transcription	Fetal Thymus	thymus
34	chr2:36801800-36813800	Strong transcription	Fetal Muscle Leg	muscle
35	chr2:36801800-36814600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:36801800-36816200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:36801800-36817200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:36801800-36818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:36802000-36818000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:36802000-36823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:36802400-36815200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:36802800-36811400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:36802800-36812400	Strong transcription	NH-A	brain
44	chr2:36803000-36810800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:36803200-36813400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr2:36803400-36812000	Strong transcription	HMEC	breast
47	chr2:36803600-36818000	Strong transcription	Dnd41	blood
48	chr2:36803800-36811400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:36803800-36814600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:36804400-36812400	Strong transcription	Adipose Nuclei	Adipose

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