Variant report

Variant	rs2973685
Chromosome Location	chr5:177759837-177759838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177757932..177760832-chr5:177771910..177774390,2	K562	blood:
2	chr5:177751727..177753386-chr5:177758828..177761752,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1110162	0.96[YRI][hapmap];0.85[AMR][1000 genomes]
rs1110163	0.88[ASW][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes]
rs1529444	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17580218	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs17641413	0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs2913788	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]
rs2913789	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2913790	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2913791	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2913793	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2913794	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2913795	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2973671	0.82[AMR][1000 genomes]
rs2973674	0.85[AMR][1000 genomes]
rs2973675	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2973676	0.93[YRI][hapmap];0.86[AMR][1000 genomes]
rs2973677	0.82[ASW][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2973678	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2973679	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2973680	0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2973681	0.91[AMR][1000 genomes]
rs2973682	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2973683	0.87[ASW][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2973684	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34688771	0.86[ASN][1000 genomes]
rs35865625	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6877633	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs748083	0.88[CHB][hapmap]
rs7713234	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs890806	0.81[AMR][1000 genomes]
rs9329142	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
12	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
rs2973685	HRH2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177749600-177761400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr5:177757400-177762400	Enhancers	Liver	Liver
3	chr5:177757600-177760400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:177757600-177760600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr5:177757600-177760600	Enhancers	Stomach Mucosa	stomach
6	chr5:177757600-177763600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:177757800-177761400	Enhancers	Gastric	stomach
8	chr5:177758000-177761400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:177758000-177761800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:177758000-177764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:177758200-177760800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:177758200-177762200	Weak transcription	Dnd41	blood
13	chr5:177758400-177760800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:177758400-177760800	Enhancers	Fetal Heart	heart
15	chr5:177758400-177762200	Weak transcription	Thymus	Thymus
16	chr5:177759000-177761400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:177759200-177761400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:177759200-177761800	Weak transcription	Fetal Thymus	thymus
19	chr5:177759200-177764000	Weak transcription	Brain Germinal Matrix	brain
20	chr5:177759200-177765000	Enhancers	Fetal Muscle Leg	muscle
21	chr5:177759400-177760000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr5:177759400-177760000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr5:177759400-177760000	Enhancers	HSMMtube	muscle
24	chr5:177759400-177760400	Weak transcription	Lung	lung
25	chr5:177759400-177760400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:177759400-177760400	Weak transcription	Spleen	Spleen
27	chr5:177759400-177760600	Weak transcription	Right Ventricle	heart
28	chr5:177759400-177762000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:177759400-177783400	Weak transcription	Right Atrium	heart
30	chr5:177759600-177760800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:177759800-177760200	Weak transcription	Placenta	Placenta
32	chr5:177759800-177761000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:177759800-177761000	Enhancers	Hela-S3	cervix
34	chr5:177759800-177762800	Weak transcription	Fetal Lung	lung
35	chr5:177759800-177765000	Weak transcription	Left Ventricle	heart

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