Variant report

Variant	rs7602412
Chromosome Location	chr2:98596331-98596332
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

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];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10200949	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10211231	0.90[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]
rs10865055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123924	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11123949	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11123966	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11690482	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11693874	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11888323	0.90[AFR][1000 genomes];0.92[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	0.80[ASN][1000 genomes]
rs12712174	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13003978	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006817	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022778	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317178	1.00[CEU][hapmap];0.91[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];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1922280	0.86[ASN][1000 genomes]
rs1922282	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2017028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100058	0.80[ASN][1000 genomes]
rs2141862	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279825	0.94[AMR][1000 genomes];0.93[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];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2309317	0.81[AFR][1000 genomes]
rs2309356	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088327	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3762593	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4274643	1.00[CEU][hapmap];0.91[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];0.91[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];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6543210	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6707924	0.82[AFR][1000 genomes]
rs6709571	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[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	0.81[ASN][1000 genomes]
rs6748927	0.81[ASN][1000 genomes]
rs7558931	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs7561104	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7562695	0.84[ASN][1000 genomes]
rs7567397	1.00[CEU][hapmap];0.91[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];0.82[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];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598116	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7605180	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308862	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs956696	0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7602412	ZAP70	cis	Nerve Tibial	GTEx
rs7602412	TMEM131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:98584600-98597000	Weak transcription	Thymus	Thymus
3	chr2:98585000-98608400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:98587400-98599600	Weak transcription	Spleen	Spleen
5	chr2:98587800-98600000	Weak transcription	Gastric	stomach
6	chr2:98588600-98598200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:98589200-98597400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:98591800-98599600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:98591800-98599600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:98592200-98606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:98592400-98599200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:98592600-98603000	Weak transcription	Ovary	ovary
13	chr2:98592600-98604600	Weak transcription	Fetal Brain Male	brain
14	chr2:98593200-98606400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:98594600-98602600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:98594800-98596600	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr2:98594800-98597000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr2:98594800-98597000	ZNF genes & repeats	Fetal Lung	lung
19	chr2:98594800-98597400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:98595000-98596400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr2:98595000-98597000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:98595000-98597000	ZNF genes & repeats	A549	lung
23	chr2:98595200-98597400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:98595400-98596400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr2:98595400-98597000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
26	chr2:98595400-98597200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:98595400-98597400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:98595600-98596800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
29	chr2:98595600-98597000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:98595600-98597000	ZNF genes & repeats	Dnd41	blood
31	chr2:98595600-98597400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr2:98595800-98596400	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr2:98595800-98596400	ZNF genes & repeats	HepG2	liver
34	chr2:98595800-98596400	ZNF genes & repeats	HSMMtube	muscle
35	chr2:98595800-98596600	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:98595800-98596600	ZNF genes & repeats	Left Ventricle	heart
37	chr2:98595800-98596600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
38	chr2:98595800-98606400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:98596000-98596400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:98596000-98597000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr2:98596000-98597000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr2:98596000-98597200	Enhancers	Stomach Mucosa	stomach
43	chr2:98596000-98598600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:98596000-98599000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:98596000-98599200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:98596000-98599400	Weak transcription	Fetal Heart	heart
47	chr2:98596000-98599600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:98596000-98599800	Weak transcription	Liver	Liver
49	chr2:98596000-98600000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:98596000-98600000	Weak transcription	Pancreas	Pancrea

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