Variant report

Variant	rs2236954
Chromosome Location	chr3:50425177-50425178
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50423026..50425468-chr3:50433598..50435342,2	K562	blood:
2	chr3:50402953..50405922-chr3:50425118..50426805,2	MCF-7	breast:
3	chr3:50419009..50422090-chr3:50424618..50428241,4	MCF-7	breast:
4	chr3:50407737..50410112-chr3:50424315..50425913,2	K562	blood:

Variant related genes	Relation type
ENSG00000007402	Chromatin interaction
ENSG00000271858	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1107265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490042	0.94[CEU][hapmap];0.80[JPT][hapmap];0.90[EUR][1000 genomes]
rs12492113	0.81[CEU][hapmap]
rs12494849	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs13087550	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1467913	0.94[CEU][hapmap]
rs1467914	0.94[CEU][hapmap];0.87[GIH][hapmap];0.82[AMR][1000 genomes]
rs2073496	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236951	0.85[YRI][hapmap];0.82[AMR][1000 genomes]
rs2236953	0.94[CEU][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs2236955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236956	0.94[CEU][hapmap];0.80[JPT][hapmap];0.90[EUR][1000 genomes]
rs2236957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236958	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2236959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2236961	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs2236962	0.86[EUR][1000 genomes]
rs2236963	0.94[CEU][hapmap];0.90[GIH][hapmap];0.86[EUR][1000 genomes]
rs2236964	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2236965	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236967	0.94[CEU][hapmap];0.90[GIH][hapmap];0.86[EUR][1000 genomes]
rs2236968	0.94[CEU][hapmap];0.90[GIH][hapmap];0.86[EUR][1000 genomes]
rs2236971	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2236973	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236975	0.94[CEU][hapmap];0.90[GIH][hapmap];0.81[EUR][1000 genomes]
rs2236979	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236981	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236984	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236987	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2236988	0.94[CEU][hapmap]
rs2282752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282756	0.94[CEU][hapmap];0.90[GIH][hapmap]
rs2282758	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2282762	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2298955	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34762184	0.87[CEU][hapmap]
rs35986136	0.87[CEU][hapmap]
rs4688719	0.94[CEU][hapmap]
rs6446206	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786523	0.94[CEU][hapmap];0.87[GIH][hapmap]
rs6787890	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs6792502	0.94[CEU][hapmap]
rs6807916	0.88[CEU][hapmap]
rs71326932	0.81[EUR][1000 genomes]
rs734767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743756	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs743757	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs743857	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs750510	0.83[CEU][hapmap]
rs762895	0.94[CEU][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.90[EUR][1000 genomes]
rs762897	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762898	0.94[CEU][hapmap];0.90[GIH][hapmap];0.80[EUR][1000 genomes]
rs763030	0.94[CEU][hapmap]
rs916217	0.94[CEU][hapmap];0.90[GIH][hapmap];0.86[EUR][1000 genomes]
rs929047	0.94[CEU][hapmap]
rs9835537	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9867588	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
8	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
9	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
10	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
11	nsv876774	chr3:50302830-50436827	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
12	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
13	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
14	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
17	nsv876778	chr3:50413707-50465518	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	nsv590271	chr3:50420554-50436716	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
19	esv989401	chr3:50424492-50426815	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50411400-50430000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:50412800-50428000	Weak transcription	Right Ventricle	heart
3	chr3:50415200-50428400	Weak transcription	Brain Anterior Caudate	brain
4	chr3:50417000-50428000	Weak transcription	Gastric	stomach
5	chr3:50419600-50426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:50420600-50425200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:50421400-50428000	Weak transcription	Esophagus	oesophagus
8	chr3:50421600-50426800	Weak transcription	Fetal Intestine Small	intestine
9	chr3:50421600-50428200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:50421800-50425600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:50422400-50428000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:50422600-50426800	Enhancers	Fetal Brain Male	brain
13	chr3:50422600-50428000	Weak transcription	Lung	lung
14	chr3:50422800-50426400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:50423200-50427200	Weak transcription	Spleen	Spleen
16	chr3:50423600-50425200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:50423800-50426000	Enhancers	Fetal Brain Female	brain
18	chr3:50424000-50431000	Enhancers	Fetal Muscle Leg	muscle
19	chr3:50424000-50433000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:50424200-50425400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:50424200-50426400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:50424400-50427000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:50424600-50425800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:50424600-50426200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:50424600-50426400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:50424800-50427200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr3:50425000-50425200	Bivalent Enhancer	Fetal Stomach	stomach
28	chr3:50425000-50425400	Flanking Active TSS	Brain Germinal Matrix	brain

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