Variant report

Variant	rs10865055
Chromosome Location	chr2:98587889-98587890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98582131..98586071-chr2:98586872..98589219,3	K562	blood:
2	chr2:98586492..98590623-chr2:98609849..98613256,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10176201	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10182941	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10200949	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10211231	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1071885	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11123924	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11123949	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123966	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11690482	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11693874	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11888323	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11899171	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12712123	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13003978	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006817	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022778	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.86[ASN][1000 genomes]
rs13405546	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1466924	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1503200	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1922280	0.86[ASN][1000 genomes]
rs1922282	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2017028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100058	0.80[ASN][1000 genomes]
rs2141862	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279825	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309316	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs2309317	0.85[AFR][1000 genomes]
rs2309356	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088327	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762593	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4560167	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6543108	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6543109	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6543161	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6543177	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6543202	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6543210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707924	0.82[AFR][1000 genomes]
rs6709571	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6719556	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6723466	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6723653	0.88[ASN][1000 genomes]
rs6744331	0.85[ASN][1000 genomes]
rs6748809	0.84[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs6748927	0.83[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs7561104	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7562695	0.84[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7574437	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7577886	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7582664	0.84[ASN][1000 genomes]
rs7586210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598116	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7602412	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605180	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308862	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs956696	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9973416	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10865055	FAM178B	cis	parietal	SCAN
rs10865055	CNNM3	cis	cerebellum	SCAN
rs10865055	ADRA2B	cis	cerebellum	SCAN
rs10865055	ZAP70	cis	Nerve Tibial	GTEx
rs10865055	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs10865055	ZAP70	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:98575000-98589000	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:98575400-98595000	Weak transcription	HSMM	muscle
7	chr2:98580000-98589800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:98581000-98589600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:98582400-98588400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:98582600-98588600	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:98582800-98588000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:98583000-98588000	Enhancers	Liver	Liver
13	chr2:98583000-98588800	Enhancers	HepG2	liver
14	chr2:98583200-98588400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:98583200-98589400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:98583600-98595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:98583800-98589200	Weak transcription	Hela-S3	cervix
18	chr2:98584200-98588400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:98584600-98590000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:98584600-98597000	Weak transcription	Thymus	Thymus
21	chr2:98585000-98608400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:98585200-98589800	Weak transcription	Primary B cells from cord blood	blood
23	chr2:98585400-98588200	Enhancers	Stomach Mucosa	stomach
24	chr2:98585400-98591200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:98585600-98588200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:98585600-98594800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:98586200-98588000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:98586600-98589200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:98586600-98589400	Weak transcription	NHDF-Ad	bronchial
30	chr2:98586600-98589600	Weak transcription	Fetal Lung	lung
31	chr2:98586800-98588200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:98586800-98588400	Enhancers	GM12878-XiMat	blood
33	chr2:98586800-98589000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:98586800-98590600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:98587000-98588000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:98587000-98594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:98587000-98595600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:98587200-98589000	Weak transcription	Fetal Intestine Small	intestine
39	chr2:98587200-98589200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:98587200-98589800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:98587200-98589800	Weak transcription	Right Atrium	heart
42	chr2:98587200-98590000	Weak transcription	Primary T cells from cord blood	blood
43	chr2:98587200-98591200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:98587400-98588400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:98587400-98588400	Weak transcription	Psoas Muscle	Psoas
46	chr2:98587400-98588600	Weak transcription	Small Intestine	intestine
47	chr2:98587400-98589000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:98587400-98589000	Weak transcription	Aorta	Aorta
49	chr2:98587400-98589000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:98587400-98589200	Weak transcription	Primary T cells fromperipheralblood	blood

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