Variant report

Variant	rs7540391
Chromosome Location	chr1:227416247-227416248
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227414219..227417070-chr1:227421056..227422767,2	K562	blood:
2	chr1:227414219..227417326-chr1:227421056..227422944,3	K562	blood:
3	chr1:227411051..227412753-chr1:227415183..227417286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228729	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10127638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10495256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12118840	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12403775	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs1319103	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1513609	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1513617	0.94[ASN][1000 genomes]
rs1849550	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1929855	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2670470	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2718191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2718214	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2718220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2718223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2813955	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2813956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2813957	0.98[EUR][1000 genomes]
rs2813977	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2953640	0.90[ASW][hapmap];0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs4146588	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4375224	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4653822	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426578	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6426584	1.00[JPT][hapmap]
rs6426596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66796195	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72753628	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72755321	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7531992	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7540155	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7540618	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9700661	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227380200-227421800	Weak transcription	Ovary	ovary
2	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
4	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
6	chr1:227405600-227421800	Weak transcription	Gastric	stomach
7	chr1:227406400-227417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
9	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
10	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:227414000-227421800	Weak transcription	Left Ventricle	heart
12	chr1:227414000-227424400	Weak transcription	Psoas Muscle	Psoas
13	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:227414200-227423400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:227414200-227424200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:227414200-227424400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:227414200-227426800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:227414200-227453800	Weak transcription	HSMM	muscle
21	chr1:227414400-227422200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:227414400-227422400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:227414400-227422400	Weak transcription	K562	blood
24	chr1:227414400-227423000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:227414400-227423000	Weak transcription	Brain Substantia Nigra	brain
26	chr1:227414400-227423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:227415400-227422200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:227415400-227424400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:227415600-227416400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:227415600-227422800	Weak transcription	HUVEC	blood vessel
33	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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