Variant report

Variant	rs4394002
Chromosome Location	chr4:106864273-106864274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10007955	0.90[YRI][hapmap]
rs10029346	0.80[CEU][hapmap];0.81[YRI][hapmap]
rs10032388	0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10033065	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10856978	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11097903	0.83[AMR][1000 genomes]
rs11930350	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12511099	1.00[EUR][1000 genomes]
rs13103583	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13107002	1.00[EUR][1000 genomes]
rs13120676	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2069092	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs28420290	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28505995	0.87[AFR][1000 genomes]
rs28540395	0.90[AFR][1000 genomes]
rs28542670	0.90[AFR][1000 genomes]
rs28690684	0.88[AFR][1000 genomes]
rs4074126	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074127	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074792	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4235416	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4264830	1.00[EUR][1000 genomes]
rs4340795	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4380529	1.00[EUR][1000 genomes]
rs4380530	0.85[EUR][1000 genomes]
rs4403054	1.00[EUR][1000 genomes]
rs4443288	0.89[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4488941	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4507363	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4511999	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4546247	0.88[EUR][1000 genomes]
rs4571330	0.95[AFR][1000 genomes]
rs4616757	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627867	0.83[AMR][1000 genomes]
rs4635819	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4643812	0.80[CEU][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs4699201	0.83[AMR][1000 genomes]
rs4699202	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4699203	0.87[AFR][1000 genomes]
rs4699204	0.93[AFR][1000 genomes]
rs58168413	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533223	1.00[CEU][hapmap]
rs6815439	0.88[AFR][1000 genomes]
rs6826402	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6826426	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6838274	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6855132	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs73839086	0.87[AFR][1000 genomes]
rs7664696	0.90[AFR][1000 genomes]
rs7669108	1.00[EUR][1000 genomes]
rs7672530	0.83[AMR][1000 genomes]
rs7673502	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7677312	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7696538	0.89[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9790337	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106831600-106878200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:106837600-106867600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:106838000-106864400	Weak transcription	Small Intestine	intestine
4	chr4:106843600-106888400	Weak transcription	Pancreas	Pancrea
5	chr4:106851200-106871800	Weak transcription	Esophagus	oesophagus
6	chr4:106853000-106879000	Weak transcription	Fetal Stomach	stomach
7	chr4:106854000-106865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:106854000-106866600	Weak transcription	Fetal Intestine Small	intestine
9	chr4:106854400-106886800	Weak transcription	GM12878-XiMat	blood
10	chr4:106854600-106866400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:106856000-106865400	Weak transcription	HSMM	muscle
12	chr4:106858400-106864400	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:106858400-106864400	Weak transcription	Right Atrium	heart
14	chr4:106858400-106871800	Weak transcription	Lung	lung
15	chr4:106859400-106868800	Strong transcription	Fetal Intestine Large	intestine
16	chr4:106859600-106865800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:106861800-106865200	Weak transcription	HSMMtube	muscle
18	chr4:106861800-106867600	Weak transcription	Aorta	Aorta
19	chr4:106862400-106867400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:106863400-106864400	Strong transcription	Fetal Lung	lung
21	chr4:106863400-106864800	Strong transcription	Fetal Kidney	kidney
22	chr4:106863600-106864600	Genic enhancers	Fetal Heart	heart
23	chr4:106863600-106864600	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr4:106863800-106864400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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