Variant report

Variant	rs2688231
Chromosome Location	chr4:8490981-8490982
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	chr4:8465664..8467583-chr4:8490405..8491928,2	K562	blood:
2	chr4:8490067..8491985-chr4:8548125..8550420,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1357481	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543246	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1880023	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1880024	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1916326	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1949733	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2010758	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2140337	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2386227	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2450475	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2631731	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2631734	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2631735	0.96[EUR][1000 genomes]
rs2631736	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631740	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631743	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631744	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2631745	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631746	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2631754	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2631756	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2631758	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2631762	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2631768	0.83[EUR][1000 genomes]
rs2688219	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2688223	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688224	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2688227	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2688233	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2688235	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2688242	0.87[AMR][1000 genomes]
rs2688243	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688247	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3103067	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3103069	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3103070	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3103071	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3103072	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3103099	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4696828	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447875	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6837429	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6845969	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6858542	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs868105	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs871768	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs940134	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs940136	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
3	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2688231	RP11-689P11.2	cis	lung	GTEx
rs2688231	TRMT44	cis	Nerve Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8473600-8501400	Weak transcription	Brain Substantia Nigra	brain
2	chr4:8475600-8491400	Weak transcription	Aorta	Aorta
3	chr4:8475800-8491800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:8478000-8500200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:8478200-8491400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:8478600-8492000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:8479200-8501400	Weak transcription	Liver	Liver
8	chr4:8479400-8491200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:8479800-8494600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:8480000-8493000	Weak transcription	Gastric	stomach
11	chr4:8480200-8498400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:8480200-8501400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:8480600-8498200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:8480800-8497400	Weak transcription	Spleen	Spleen
15	chr4:8481400-8491800	Weak transcription	Esophagus	oesophagus
16	chr4:8481400-8495200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:8481400-8496800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:8481400-8501400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:8481600-8493200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:8481800-8491800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:8481800-8497400	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:8482200-8495000	Weak transcription	Brain Germinal Matrix	brain
23	chr4:8482200-8501400	Weak transcription	Primary T cells from cord blood	blood
24	chr4:8483800-8494400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:8484200-8497000	Weak transcription	Placenta	Placenta
26	chr4:8489000-8492200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:8490200-8491000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr4:8490400-8491000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:8490400-8491000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:8490400-8491000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:8490400-8491000	Strong transcription	Fetal Brain Female	brain
32	chr4:8490400-8491000	ZNF genes & repeats	Lung	lung
33	chr4:8490400-8491000	Strong transcription	Ovary	ovary
34	chr4:8490400-8491200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
35	chr4:8490400-8491200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
36	chr4:8490400-8491200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
37	chr4:8490400-8492000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:8490600-8491000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr4:8490600-8492000	Strong transcription	Fetal Stomach	stomach
40	chr4:8490800-8491200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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