Variant report

Variant	rs2913788
Chromosome Location	chr5:177757764-177757765
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1110162	0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs1110163	0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1529444	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17580218	0.86[ASN][1000 genomes]
rs17641413	1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs2913789	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913790	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2913791	0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2913793	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2913794	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2913795	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2973671	0.84[AMR][1000 genomes]
rs2973674	0.87[AMR][1000 genomes]
rs2973675	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2973676	0.82[YRI][hapmap];0.88[AMR][1000 genomes]
rs2973677	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2973678	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2973679	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973680	0.81[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2973681	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973682	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2973683	0.87[ASW][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2973684	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2973685	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34688771	0.86[ASN][1000 genomes]
rs35865625	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6877633	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7713234	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs890806	0.83[AMR][1000 genomes]

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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
5	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv883203	chr5:177682664-177766183	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv883205	chr5:177684682-177777888	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv883206	chr5:177684682-177796121	Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv883208	chr5:177692247-177757764	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv1027165	chr5:177693601-177843314	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv984572	chr5:177737015-177763963	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2913788	HRH2	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177739800-177757800	Weak transcription	Gastric	stomach
2	chr5:177749600-177761400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr5:177751400-177759600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:177752000-177758200	Weak transcription	Fetal Intestine Large	intestine
5	chr5:177752000-177758800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:177752600-177758000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:177753800-177757800	Weak transcription	Fetal Intestine Small	intestine
8	chr5:177753800-177758200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:177754000-177759800	Bivalent Enhancer	Fetal Stomach	stomach
10	chr5:177754400-177758200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:177755200-177759000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr5:177755600-177759000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:177755800-177758000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr5:177756200-177757800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:177756400-177759800	Enhancers	Placenta	Placenta
16	chr5:177756600-177759800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr5:177756800-177759600	Enhancers	Brain Cingulate Gyrus	brain
18	chr5:177757000-177757800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:177757000-177758400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr5:177757000-177759400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:177757000-177759400	Enhancers	Spleen	Spleen
22	chr5:177757000-177759600	Enhancers	Brain Hippocampus Middle	brain
23	chr5:177757000-177759600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:177757000-177759600	Enhancers	Brain Substantia Nigra	brain
25	chr5:177757200-177757800	Enhancers	Fetal Heart	heart
26	chr5:177757200-177758200	Enhancers	Brain Anterior Caudate	brain
27	chr5:177757200-177758400	Enhancers	Thymus	Thymus
28	chr5:177757200-177759200	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr5:177757200-177759200	Enhancers	Fetal Thymus	thymus
30	chr5:177757200-177759400	Enhancers	Brain Angular Gyrus	brain
31	chr5:177757200-177759400	Enhancers	Lung	lung
32	chr5:177757200-177759600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:177757200-177759600	Enhancers	Esophagus	oesophagus
34	chr5:177757200-177759800	Enhancers	Fetal Lung	lung
35	chr5:177757400-177759400	Enhancers	Right Atrium	heart
36	chr5:177757400-177762400	Enhancers	Liver	Liver
37	chr5:177757600-177757800	Enhancers	Fetal Kidney	kidney
38	chr5:177757600-177758000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr5:177757600-177758000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr5:177757600-177758200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr5:177757600-177758200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr5:177757600-177758200	Enhancers	Dnd41	blood
43	chr5:177757600-177758200	Enhancers	Hela-S3	cervix
44	chr5:177757600-177758400	Enhancers	Primary T cells from cord blood	blood
45	chr5:177757600-177759000	Enhancers	HSMMtube	muscle
46	chr5:177757600-177759400	Enhancers	Pancreas	Pancrea
47	chr5:177757600-177759400	Enhancers	Psoas Muscle	Psoas
48	chr5:177757600-177759400	Enhancers	Right Ventricle	heart
49	chr5:177757600-177759600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr5:177757600-177759800	Enhancers	Left Ventricle	heart

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