Variant report

Variant	rs4775988
Chromosome Location	chr15:52237091-52237092
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	chr15:52234756..52237147-chr15:52240029..52242355,2	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1025185	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10519323	1.00[EUR][1000 genomes]
rs10519325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10519326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12438469	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12442283	1.00[EUR][1000 genomes]
rs1378891	1.00[EUR][1000 genomes]
rs1426085	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1426086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16964523	0.86[JPT][hapmap]
rs16964555	1.00[YRI][hapmap]
rs16964561	1.00[YRI][hapmap]
rs16964596	1.00[YRI][hapmap]
rs17649047	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs17649178	1.00[EUR][1000 genomes]
rs17649255	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17649391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17649692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649801	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17705530	1.00[EUR][1000 genomes]
rs17705649	1.00[EUR][1000 genomes]
rs17705685	1.00[EUR][1000 genomes]
rs17705889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17706076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2052707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162224	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2263946	0.85[ASN][1000 genomes]
rs2436664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2470609	0.90[ASN][1000 genomes]
rs2470613	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554310	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554311	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554317	0.90[ASN][1000 genomes]
rs2554318	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554321	0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2554323	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554325	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554326	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554330	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2554333	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554341	0.82[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2554351	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554352	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554356	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570219	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570220	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570221	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570225	0.92[ASN][1000 genomes]
rs2570227	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570234	0.90[ASN][1000 genomes]
rs2570242	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570244	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570246	0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2570247	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2570256	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570257	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570259	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570261	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570262	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2570267	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570273	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570274	1.00[EUR][1000 genomes]
rs2593165	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593175	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593176	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593180	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623246	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2623250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623252	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623253	0.90[ASN][1000 genomes]
rs2623257	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623260	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623264	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623267	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623268	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623269	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623277	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623278	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623287	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623293	0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2899483	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2916174	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2959297	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2959303	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099570	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34407523	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794533	1.00[EUR][1000 genomes]
rs3794537	1.00[EUR][1000 genomes]
rs4774600	1.00[EUR][1000 genomes]
rs4774601	1.00[EUR][1000 genomes]
rs4775979	1.00[EUR][1000 genomes]
rs4775987	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775989	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166322	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs7170429	1.00[EUR][1000 genomes]
rs7170700	1.00[EUR][1000 genomes]
rs7173661	1.00[EUR][1000 genomes]
rs7179139	1.00[EUR][1000 genomes]
rs73411105	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74013606	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8024441	1.00[EUR][1000 genomes]
rs8026507	1.00[EUR][1000 genomes]
rs8027426	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs8042310	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs919057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs990666	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
4	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:52210000-52239000	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:52211600-52237600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:52211600-52239200	Weak transcription	Right Ventricle	heart
9	chr15:52212400-52241600	Weak transcription	Small Intestine	intestine
10	chr15:52216000-52238600	Weak transcription	Pancreas	Pancrea
11	chr15:52217200-52238400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:52217200-52238800	Weak transcription	Brain Angular Gyrus	brain
13	chr15:52217600-52238800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr15:52217800-52237400	Weak transcription	Aorta	Aorta
15	chr15:52217800-52237400	Weak transcription	Brain Anterior Caudate	brain
16	chr15:52217800-52239000	Weak transcription	Gastric	stomach
17	chr15:52218000-52243200	Weak transcription	Fetal Heart	heart
18	chr15:52222600-52259800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:52223200-52245400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:52224000-52237400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:52224200-52237200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:52226000-52255200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:52226200-52242600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:52226200-52254800	Strong transcription	Thymus	Thymus
25	chr15:52226200-52255000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:52226800-52237200	Weak transcription	Spleen	Spleen
28	chr15:52227400-52255000	Strong transcription	Liver	Liver
29	chr15:52227400-52258400	Strong transcription	Dnd41	blood
30	chr15:52227800-52255000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr15:52228400-52238400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:52229200-52238200	Weak transcription	Brain Germinal Matrix	brain
33	chr15:52229400-52249000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:52229800-52254200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:52230000-52237400	Weak transcription	Ovary	ovary
36	chr15:52230200-52238600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:52230800-52237400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:52230800-52237600	Weak transcription	Adipose Nuclei	Adipose
39	chr15:52232200-52237400	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:52232200-52238600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:52232200-52238800	Weak transcription	K562	blood
42	chr15:52232200-52239000	Weak transcription	HUVEC	blood vessel
43	chr15:52232800-52256000	Strong transcription	Fetal Muscle Leg	muscle
44	chr15:52233000-52258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:52233200-52250800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr15:52233200-52255200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr15:52233200-52255200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:52233400-52248000	Strong transcription	Primary T cells from cord blood	blood
49	chr15:52233600-52258000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr15:52233800-52237400	Weak transcription	Fetal Intestine Small	intestine

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