Variant report

Variant	rs2850994
Chromosome Location	chr4:102129299-102129300
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102127770..102129631-chr4:102130414..102132314,2	MCF-7	breast:
2	chr4:102129139..102132021-chr4:102226843..102229507,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1021965	0.84[ASN][1000 genomes]
rs1157038	0.89[CEU][hapmap]
rs1354785	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1395475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1395476	0.89[CEU][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1506799	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506800	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506803	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506804	0.89[CEU][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1543856	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17030851	0.80[ASN][1000 genomes]
rs2135609	0.89[CEU][hapmap]
rs2135610	0.89[CEU][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2135612	0.89[CEU][hapmap]
rs2174683	0.80[CHD][hapmap]
rs2659503	0.89[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2659504	0.89[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2659505	0.82[CEU][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2659506	0.88[ASW][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2659508	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2659509	0.88[ASW][hapmap];0.81[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659511	0.88[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659512	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659513	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659522	0.88[CEU][hapmap]
rs2659525	0.89[CEU][hapmap]
rs2659530	0.89[CEU][hapmap]
rs2659531	0.88[CEU][hapmap]
rs2659532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659533	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659534	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659537	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659538	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659539	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659540	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659541	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2659542	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2850980	0.84[ASN][1000 genomes]
rs2850981	0.89[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2850982	0.89[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2850985	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850987	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850989	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850990	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2850991	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850995	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850998	0.89[CEU][hapmap]
rs2851003	0.89[CEU][hapmap]
rs3804366	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4478191	0.85[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs73833252	0.82[ASN][1000 genomes]
rs931871	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs970071	0.89[CEU][hapmap]

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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102113800-102131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr4:102118000-102132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:102120000-102131400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:102121800-102131200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:102121800-102132600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:102122000-102132400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr4:102123000-102129400	Weak transcription	Right Ventricle	heart
8	chr4:102123200-102131400	Weak transcription	Aorta	Aorta
9	chr4:102123200-102131600	Weak transcription	Small Intestine	intestine
10	chr4:102123200-102132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:102123200-102132200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:102123200-102132200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:102123200-102132400	Weak transcription	NHEK	skin
14	chr4:102123200-102133400	Weak transcription	Psoas Muscle	Psoas
15	chr4:102123200-102133400	Weak transcription	Right Atrium	heart
16	chr4:102123400-102132800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:102124200-102132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:102125200-102129600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:102125800-102129600	Enhancers	Dnd41	blood
20	chr4:102127200-102132200	Weak transcription	HSMM	muscle
21	chr4:102127400-102129400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:102127400-102132000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:102127400-102132000	Weak transcription	NH-A	brain
24	chr4:102127400-102132200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:102127400-102132200	Weak transcription	HMEC	breast
26	chr4:102127400-102132200	Weak transcription	NHDF-Ad	bronchial
27	chr4:102127400-102132600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:102127800-102131600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:102127800-102131800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:102127800-102132200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:102127800-102132200	Weak transcription	Osteobl	bone
32	chr4:102128000-102129400	Weak transcription	Brain Anterior Caudate	brain
33	chr4:102128000-102129400	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:102128000-102138200	Weak transcription	Primary B cells from cord blood	blood
35	chr4:102128200-102130600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:102128200-102131400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:102128200-102132000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:102128400-102129400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:102128400-102129400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:102128800-102129400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:102129000-102129400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:102129000-102131200	Enhancers	A549	lung
43	chr4:102129000-102140400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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