Variant report

Variant	rs12329128
Chromosome Location	chr2:97284917-97284918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1011040	0.92[CEU][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10184209	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10194468	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12477963	0.89[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs12717781	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12717782	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992413	0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13007343	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13019986	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13029764	0.92[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17685664	0.80[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes]
rs17685766	0.85[AMR][1000 genomes]
rs2292939	1.00[JPT][hapmap]
rs2314109	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2579502	0.88[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs2579505	0.81[CEU][hapmap]
rs2708977	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2708978	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34029026	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35071802	0.84[GIH][hapmap]
rs749027	0.84[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs7572249	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12329128	FAM178B	cis	parietal	SCAN
rs12329128	ADRA2B	cis	cerebellum	SCAN
rs12329128	TMEM127	cis	parietal	SCAN
rs12329128	LOC285033	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97256600-97287000	Strong transcription	Dnd41	blood
2	chr2:97257600-97286400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:97257800-97286800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:97258200-97286400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:97258200-97302800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:97261200-97301600	Strong transcription	Fetal Thymus	thymus
7	chr2:97266200-97287600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr2:97266200-97291000	Strong transcription	Fetal Stomach	stomach
9	chr2:97268600-97285800	Strong transcription	Fetal Intestine Large	intestine
10	chr2:97268800-97287400	Strong transcription	Fetal Intestine Small	intestine
11	chr2:97273200-97291800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:97273400-97287000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:97275000-97298600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:97276800-97285000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:97277200-97291800	Weak transcription	Stomach Mucosa	stomach
16	chr2:97278600-97293200	Weak transcription	Small Intestine	intestine
17	chr2:97279800-97293200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:97280800-97286400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:97281000-97286000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:97281200-97286600	Strong transcription	Primary T cells from cord blood	blood
21	chr2:97281200-97287600	Strong transcription	A549	lung
22	chr2:97281400-97285600	Strong transcription	Thymus	Thymus
23	chr2:97281400-97285800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr2:97281400-97286000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:97281400-97286600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:97281600-97285600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:97281600-97285600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:97281600-97285600	Strong transcription	Primary B cells from cord blood	blood
29	chr2:97281600-97286000	Strong transcription	K562	blood
30	chr2:97281600-97286400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr2:97281600-97291800	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:97281800-97285800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr2:97281800-97285800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:97281800-97285800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:97281800-97286400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr2:97281800-97286600	Strong transcription	Fetal Brain Female	brain
37	chr2:97282200-97285400	Strong transcription	Brain Germinal Matrix	brain
38	chr2:97282400-97285000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:97282400-97285400	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr2:97282400-97285600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:97282400-97285800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:97282600-97285200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:97282600-97285800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:97283000-97285600	Strong transcription	Spleen	Spleen
45	chr2:97283000-97286400	Strong transcription	HepG2	liver
46	chr2:97283000-97288000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:97283000-97288400	Weak transcription	Right Atrium	heart
48	chr2:97283000-97293800	Weak transcription	Fetal Heart	heart
49	chr2:97283000-97296400	Weak transcription	Psoas Muscle	Psoas
50	chr2:97283200-97293400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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