Variant report

Variant	rs1877241
Chromosome Location	chr15:83435828-83435829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83425158..83429162-chr15:83434771..83437129,3	K562	blood:
2	chr15:83432559..83435214-chr15:83435455..83437217,3	MCF-7	breast:
3	chr15:83419437..83421687-chr15:83435711..83437467,2	K562	blood:
4	chr15:83428179..83430469-chr15:83435765..83438520,3	MCF-7	breast:
5	chr15:83417706..83421597-chr15:83434237..83437935,4	MCF-7	breast:
6	chr15:83434522..83436692-chr15:83477124..83479889,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction
ENSG00000156232	Chromatin interaction
ENSG00000252690	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1105867	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12385964	0.94[CEU][hapmap]
rs1256429	0.94[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs1256451	0.94[CEU][hapmap]
rs1256452	0.93[CEU][hapmap]
rs1256455	1.00[CEU][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs12905235	0.84[CEU][hapmap]
rs12910279	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914161	0.84[EUR][1000 genomes]
rs1553883	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1553885	0.91[JPT][hapmap];1.00[LWK][hapmap]
rs2089844	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2379992	0.84[EUR][1000 genomes]
rs2379993	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2890313	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2928572	0.94[CEU][hapmap]
rs4238539	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7163402	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7163840	0.91[JPT][hapmap]
rs7178459	0.82[JPT][hapmap]
rs8038679	0.94[CEU][hapmap]
rs8039001	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	esv3346074	chr15:83422947-83456222	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1877241	EFTUD1	cis	cerebellum	SCAN
rs1877241	WHAMM	cis	Adipose Subcutaneous	GTEx
rs1877241	RPS17	Cis_1M	lymphoblastoid	RTeQTL
rs1877241	BTBD1	cis	parietal	SCAN
rs1877241	BTBD1	cis	cerebellum	SCAN
rs1877241	PACS2	trans	cerebellum	SCAN
rs1877241	RASGRF1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83420400-83436400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:83422400-83436800	Strong transcription	Primary T cells from cord blood	blood
3	chr15:83425000-83447800	Weak transcription	Fetal Brain Male	brain
4	chr15:83425200-83436200	Weak transcription	Colonic Mucosa	Colon
5	chr15:83427800-83437200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:83427800-83442200	Weak transcription	Brain Substantia Nigra	brain
7	chr15:83428000-83436000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:83428000-83436400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:83428000-83438200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr15:83428000-83440400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:83428000-83440400	Weak transcription	Esophagus	oesophagus
12	chr15:83428000-83441000	Weak transcription	K562	blood
13	chr15:83428000-83442200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:83428200-83437200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:83428200-83437600	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:83428200-83437800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:83428200-83439600	Weak transcription	HMEC	breast
18	chr15:83428200-83440200	Weak transcription	NHEK	skin
19	chr15:83428400-83437200	Weak transcription	Hela-S3	cervix
20	chr15:83428400-83440200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:83429200-83436600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr15:83429400-83437200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:83429600-83437600	Weak transcription	Fetal Thymus	thymus
24	chr15:83430800-83436800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:83430800-83437000	Strong transcription	Brain Germinal Matrix	brain
26	chr15:83431200-83437200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:83431200-83437200	Weak transcription	HSMMtube	muscle
28	chr15:83431200-83438800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:83431400-83437400	Weak transcription	NH-A	brain
30	chr15:83431400-83437600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:83431400-83437600	Weak transcription	Osteobl	bone
32	chr15:83431600-83437400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:83431600-83437400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:83431600-83437400	Weak transcription	HSMM	muscle
35	chr15:83432000-83436800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:83433400-83436800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:83433600-83436400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:83433600-83436600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:83433600-83436800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr15:83433600-83437000	Strong transcription	Fetal Stomach	stomach
41	chr15:83433800-83437200	Strong transcription	Fetal Intestine Small	intestine
42	chr15:83434000-83436200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:83434000-83436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:83434200-83438000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:83434200-83438000	Weak transcription	Aorta	Aorta
46	chr15:83434200-83441200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:83434400-83436000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:83434400-83436000	Weak transcription	Right Ventricle	heart
49	chr15:83434400-83437400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:83434400-83437400	Weak transcription	HepG2	liver

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