Variant report

Variant	rs2813950
Chromosome Location	chr1:227426072-227426073
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	chr1:227425043..227428027-chr1:227428390..227430436,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD4-6	chr1:227425831-227426320	NONHSAT009918

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10495253	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916104	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12039370	0.82[EUR][1000 genomes]
rs12139758	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs1483	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2102634	0.82[EUR][1000 genomes]
rs2482454	0.80[AMR][1000 genomes]
rs2670462	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670471	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2718193	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2813947	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2813948	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2813965	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2813967	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2813969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2813970	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3754418	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4351610	0.82[EUR][1000 genomes]
rs4500279	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4653813	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488104	0.80[AMR][1000 genomes]
rs498020	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs56219094	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61834571	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6662583	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6682472	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6685823	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs6692080	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6697665	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689094	0.80[AMR][1000 genomes]
rs694740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes]
rs7412928	0.82[EUR][1000 genomes]
rs7512409	0.89[ASW][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521110	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7523167	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543579	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7549520	0.83[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
4	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
5	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
6	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:227414200-227426800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:227414200-227453800	Weak transcription	HSMM	muscle
12	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
17	chr1:227422000-227430800	Weak transcription	Ovary	ovary
18	chr1:227422600-227430800	Weak transcription	Gastric	stomach
19	chr1:227423000-227426800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:227423000-227432400	Weak transcription	Small Intestine	intestine
21	chr1:227423200-227427400	Weak transcription	A549	lung
22	chr1:227423400-227426400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:227423600-227426800	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:227423600-227428800	Weak transcription	Liver	Liver
25	chr1:227423600-227430600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:227423600-227430800	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:227423600-227431400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:227423600-227432000	Weak transcription	Brain Substantia Nigra	brain
29	chr1:227423800-227426400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:227424000-227428200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:227424000-227428200	Weak transcription	K562	blood
32	chr1:227424000-227430800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:227424600-227430800	Weak transcription	NHEK	skin
34	chr1:227424800-227430600	Weak transcription	Psoas Muscle	Psoas
35	chr1:227424800-227430800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:227424800-227432600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:227424800-227440800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:227425200-227432400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:227425400-227430600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:227425400-227430800	Weak transcription	HUVEC	blood vessel
41	chr1:227425400-227445200	Weak transcription	Osteobl	bone
42	chr1:227426000-227432400	Weak transcription	Left Ventricle	heart

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