Variant report

Variant	rs2374171
Chromosome Location	chr12:31856332-31856333
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1072778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743763	0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771864	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843994	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10843998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051539	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051550	0.82[AMR][1000 genomes]
rs11051553	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1115971	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12303424	0.87[CEU][hapmap]
rs12316119	0.95[ASN][1000 genomes]
rs12818390	0.92[CEU][hapmap]
rs12819673	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2200232	0.94[ASN][1000 genomes]
rs2388926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4272863	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7295568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73090337	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73090387	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7309916	0.91[ASN][1000 genomes]
rs7953032	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7966525	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7968792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7970095	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7971803	0.83[EUR][1000 genomes]
rs7980264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs900609	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs900610	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2374171	REP15	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31822600-31862000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:31822600-31874200	Weak transcription	Right Ventricle	heart
3	chr12:31827000-31871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:31835600-31860200	Weak transcription	Fetal Kidney	kidney
5	chr12:31836000-31857600	Weak transcription	A549	lung
6	chr12:31837000-31859400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:31837200-31860400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:31837200-31865000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:31838600-31881000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:31839800-31871800	Weak transcription	Gastric	stomach
11	chr12:31840200-31858200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:31840200-31859600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:31840200-31861800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:31841200-31857800	Weak transcription	Brain Angular Gyrus	brain
15	chr12:31841200-31860400	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:31841600-31857200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:31841600-31860200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:31841600-31870000	Weak transcription	Pancreas	Pancrea
19	chr12:31842000-31860200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:31844600-31871800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:31845600-31860400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:31846400-31860200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:31846400-31860200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:31846400-31862400	Weak transcription	Aorta	Aorta
25	chr12:31846400-31871800	Weak transcription	Lung	lung
26	chr12:31846600-31860200	Weak transcription	Fetal Lung	lung
27	chr12:31847000-31857600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:31847200-31857400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:31847800-31860200	Weak transcription	Fetal Intestine Small	intestine
30	chr12:31847800-31860400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:31848200-31859600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:31848800-31860200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:31849000-31880000	Weak transcription	Psoas Muscle	Psoas
34	chr12:31849200-31860200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:31849600-31860800	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:31850800-31867600	Weak transcription	Brain Substantia Nigra	brain
37	chr12:31851000-31860200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:31851000-31880800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr12:31851600-31860800	Weak transcription	Liver	Liver
40	chr12:31851600-31863200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr12:31852800-31859200	Weak transcription	Fetal Stomach	stomach
42	chr12:31852800-31860200	Weak transcription	Brain Germinal Matrix	brain
43	chr12:31852800-31861800	Weak transcription	Left Ventricle	heart
44	chr12:31852800-31871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:31852800-31879600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:31853000-31859400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:31853000-31859600	Weak transcription	Fetal Brain Female	brain
48	chr12:31853000-31860000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:31853000-31860200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:31853000-31860200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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