Variant report

Variant	rs9812561
Chromosome Location	chr3:135762510-135762511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:135683095..135685593-chr3:135759978..135762786,2	MCF-7	breast:
2	chr3:135637017..135639088-chr3:135760171..135763131,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073711	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10048942	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10049233	0.84[ASN][1000 genomes]
rs10512973	1.00[CHB][hapmap]
rs10512981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10935175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13072596	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082684	0.84[ASN][1000 genomes]
rs13097946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325914	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434196	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1403766	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1403770	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1523595	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523596	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523597	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568349	0.93[ASN][1000 genomes]
rs16843509	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17196987	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17250445	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204259	0.93[ASN][1000 genomes]
rs28449384	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28576629	0.84[ASN][1000 genomes]
rs34311570	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34409306	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34522617	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34767379	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35257855	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36039354	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4073308	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56807950	0.93[ASN][1000 genomes]
rs59063369	0.93[ASN][1000 genomes]
rs66544356	0.93[ASN][1000 genomes]
rs67039922	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773469	0.93[ASN][1000 genomes]
rs6774289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775778	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6779603	0.93[ASN][1000 genomes]
rs6786769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6803447	1.00[CHB][hapmap]
rs6807058	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6807242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807565	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6809006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810223	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336046	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73222222	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7427833	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7433567	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7609938	0.93[ASN][1000 genomes]
rs7621331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626676	0.93[ASN][1000 genomes]
rs7628848	0.84[ASN][1000 genomes]
rs7638129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7640153	0.93[ASN][1000 genomes]
rs7641070	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7643661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289502	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808979	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813082	0.93[ASN][1000 genomes]
rs9814557	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9819988	0.93[ASN][1000 genomes]
rs9824558	0.93[ASN][1000 genomes]
rs9825239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9826806	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9829476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9833470	1.00[CHB][hapmap]
rs9833799	0.93[ASN][1000 genomes]
rs9834104	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834624	1.00[JPT][hapmap]
rs9836374	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836758	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9837355	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9839259	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9842840	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842864	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843725	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9846137	0.96[CEU][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848322	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9849088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9851361	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853577	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9854494	1.00[JPT][hapmap]
rs9862264	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862743	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9862763	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862777	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9864247	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9864514	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864656	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9864775	1.00[JPT][hapmap]
rs9868246	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870581	1.00[JPT][hapmap]
rs9872542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875948	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9876837	0.93[ASN][1000 genomes]
rs9877082	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877217	0.81[EUR][1000 genomes]
rs9880721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883808	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135721800-135763600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:135727800-135769400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:135738000-135775800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:135738400-135763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:135738400-135763600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:135739800-135767800	Weak transcription	NHDF-Ad	bronchial
7	chr3:135741000-135763600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:135742000-135763200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:135742000-135763600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:135742200-135763600	Weak transcription	Fetal Intestine Small	intestine
11	chr3:135742200-135763600	Weak transcription	NHEK	skin
12	chr3:135742800-135774200	Weak transcription	HMEC	breast
13	chr3:135744200-135763600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:135746200-135790000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:135746400-135763600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:135747800-135763600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:135748400-135763000	Weak transcription	NH-A	brain
18	chr3:135748400-135763200	Weak transcription	Fetal Intestine Large	intestine
19	chr3:135748400-135763200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:135748400-135763400	Weak transcription	HSMMtube	muscle
21	chr3:135748400-135763600	Weak transcription	Colonic Mucosa	Colon
22	chr3:135748400-135763800	Weak transcription	NHLF	lung
23	chr3:135748600-135763000	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:135748600-135763200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:135748600-135763200	Weak transcription	Esophagus	oesophagus
26	chr3:135749000-135763200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:135749000-135763600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:135749000-135763600	Weak transcription	Pancreas	Pancrea
29	chr3:135749400-135763000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:135750200-135763600	Weak transcription	Fetal Lung	lung
31	chr3:135750400-135772800	Weak transcription	Brain Substantia Nigra	brain
32	chr3:135750800-135775800	Weak transcription	Liver	Liver
33	chr3:135751200-135763200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:135753200-135764400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:135753800-135763200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:135753800-135764400	Weak transcription	Fetal Kidney	kidney
37	chr3:135754400-135763200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:135754800-135763600	Weak transcription	Brain Germinal Matrix	brain
39	chr3:135755200-135801400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:135755400-135763600	Weak transcription	Fetal Brain Female	brain
41	chr3:135755600-135763200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:135756000-135763200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:135756600-135763000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:135757000-135763000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:135757200-135763600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:135757400-135765000	Strong transcription	Fetal Stomach	stomach
47	chr3:135757800-135763800	Weak transcription	Osteobl	bone
48	chr3:135758000-135763600	Weak transcription	Right Ventricle	heart
49	chr3:135758000-135766400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:135758200-135763600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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