Variant report

Variant	rs9840416
Chromosome Location	chr3:100474366-100474367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100468053..100471019-chr3:100472317..100474592,2	MCF-7	breast:
2	chr3:100474203..100477439-chr3:100482116..100484278,3	K562	blood:
3	chr3:100473925..100475796-chr3:100476025..100478809,2	MCF-7	breast:

Extended variants
information (count: 165 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:158)

rs_ID	r²[population]
rs1027703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10451918	1.00[CEU][hapmap]
rs1144116	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1144117	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1144118	0.84[EUR][1000 genomes]
rs1144119	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1144121	0.84[EUR][1000 genomes]
rs1145344	0.84[EUR][1000 genomes]
rs1319005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13315123	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13316513	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13317522	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13317752	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13318765	0.83[AMR][1000 genomes]
rs13318793	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13319530	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13325014	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13326828	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13327329	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13433681	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13433684	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13434023	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842455	0.91[EUR][1000 genomes]
rs16842458	0.91[EUR][1000 genomes]
rs16842471	0.91[EUR][1000 genomes]
rs16842472	0.91[EUR][1000 genomes]
rs16842478	0.91[EUR][1000 genomes]
rs16842638	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16842679	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2128224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128225	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2128226	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28380383	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28469597	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28523825	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28530760	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35606932	0.91[EUR][1000 genomes]
rs35648279	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41272969	0.91[EUR][1000 genomes]
rs41272973	0.91[EUR][1000 genomes]
rs41272977	0.91[EUR][1000 genomes]
rs41272979	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41272989	0.91[EUR][1000 genomes]
rs41273547	0.91[EUR][1000 genomes]
rs4317136	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55865709	0.91[EUR][1000 genomes]
rs56254963	0.91[EUR][1000 genomes]
rs56384617	0.91[EUR][1000 genomes]
rs57687306	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57808154	0.91[EUR][1000 genomes]
rs58073790	0.91[EUR][1000 genomes]
rs58121738	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59374249	0.91[EUR][1000 genomes]
rs60162187	0.83[AMR][1000 genomes]
rs60359060	0.91[EUR][1000 genomes]
rs6769874	1.00[MEX][hapmap]
rs72919417	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72919423	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919426	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919429	0.83[AMR][1000 genomes]
rs72919433	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928625	0.83[AMR][1000 genomes]
rs72928626	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928628	0.83[AMR][1000 genomes]
rs72928630	0.83[AMR][1000 genomes]
rs72928632	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928634	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928641	0.83[AMR][1000 genomes]
rs72928658	0.83[AMR][1000 genomes]
rs72928662	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928677	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928680	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928681	0.83[AMR][1000 genomes]
rs72928697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72928991	0.83[AMR][1000 genomes]
rs72929000	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72930614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930638	0.83[AMR][1000 genomes]
rs72930658	0.91[EUR][1000 genomes]
rs72930661	0.91[EUR][1000 genomes]
rs72930666	0.91[EUR][1000 genomes]
rs72930669	0.91[EUR][1000 genomes]
rs72930671	0.91[EUR][1000 genomes]
rs72930673	0.91[EUR][1000 genomes]
rs72930674	0.91[EUR][1000 genomes]
rs72930679	0.91[EUR][1000 genomes]
rs72930703	0.83[AMR][1000 genomes]
rs72930713	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930716	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930730	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930734	0.83[AMR][1000 genomes]
rs7628074	0.91[EUR][1000 genomes]
rs7628965	0.91[EUR][1000 genomes]
rs7637207	0.91[EUR][1000 genomes]
rs7647983	0.91[EUR][1000 genomes]
rs9290170	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9290213	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9631470	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs967308	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs967309	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9809520	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs9811997	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813673	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813730	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9817424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9817550	0.83[AMR][1000 genomes]
rs9817756	0.83[AMR][1000 genomes]
rs9817778	1.00[CEU][hapmap]
rs9818055	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9818126	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9822139	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9823506	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9824297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9825075	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9826446	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828249	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9832907	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833043	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834987	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839133	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842040	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9843775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9849252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9850735	0.83[AMR][1000 genomes]
rs9851573	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9853377	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853496	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853591	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9853596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855255	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs9856442	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9856776	1.00[EUR][1000 genomes]
rs9859204	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9859445	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9859523	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9859730	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861416	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9864113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9865004	0.83[AMR][1000 genomes]
rs9866866	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9867888	1.00[CEU][hapmap]
rs9868472	0.83[AMR][1000 genomes]
rs9870028	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9871767	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9876678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9877317	0.91[EUR][1000 genomes]
rs9877865	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878155	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9879396	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9881780	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9881943	1.00[EUR][1000 genomes]
rs9883418	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv2751973	chr3:100354170-100476713	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv2751974	chr3:100354170-100476713	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100429800-100475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:100432400-100474400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:100434400-100478200	Weak transcription	Spleen	Spleen
4	chr3:100436000-100474400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:100437600-100475000	Strong transcription	Placenta	Placenta
6	chr3:100437800-100474400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr3:100441000-100474400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:100444600-100474400	Strong transcription	HSMM	muscle
10	chr3:100445400-100475600	Weak transcription	Pancreas	Pancrea
11	chr3:100447600-100477200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:100448600-100474400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
14	chr3:100453200-100479000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:100457200-100474800	Strong transcription	NHDF-Ad	bronchial
16	chr3:100457200-100480200	Weak transcription	Brain Angular Gyrus	brain
17	chr3:100459200-100474600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:100459400-100478200	Weak transcription	Fetal Stomach	stomach
19	chr3:100463000-100474400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:100463000-100474400	Strong transcription	Adipose Nuclei	Adipose
21	chr3:100463600-100474800	Strong transcription	HSMMtube	muscle
22	chr3:100465600-100478000	Weak transcription	Aorta	Aorta
23	chr3:100465600-100478000	Weak transcription	Fetal Heart	heart
24	chr3:100467000-100474400	Strong transcription	Primary T cells from cord blood	blood
25	chr3:100467400-100474400	Weak transcription	Fetal Brain Female	brain
26	chr3:100467400-100475800	Weak transcription	Thymus	Thymus
27	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
28	chr3:100468200-100488600	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:100469000-100475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:100469400-100480200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:100469600-100479200	Weak transcription	Fetal Brain Male	brain
32	chr3:100469800-100477600	Weak transcription	K562	blood
33	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
36	chr3:100470600-100474600	Strong transcription	Left Ventricle	heart
37	chr3:100471000-100474600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr3:100471000-100476000	Weak transcription	HUVEC	blood vessel
39	chr3:100471000-100477600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:100471000-100495800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:100471200-100478200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:100471200-100480200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:100471400-100474400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:100471600-100475600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:100471600-100478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:100471600-100500400	Weak transcription	Lung	lung
47	chr3:100471800-100475200	Weak transcription	NH-A	brain
48	chr3:100471800-100475800	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:100471800-100479400	Weak transcription	Fetal Kidney	kidney
50	chr3:100471800-100486200	Weak transcription	Brain Substantia Nigra	brain

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