Variant report

Variant	rs2242477
Chromosome Location	chr7:48017965-48017966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:48017535..48019169-chr7:48128413..48129998,2	K562	blood:
2	chr7:48016950..48019113-chr7:48039129..48042039,2	K562	blood:
3	chr7:48017568..48020341-chr7:48128356..48131105,2	MCF-7	breast:
4	chr7:48017456..48020295-chr7:48126750..48129913,5	K562	blood:

Variant related genes	Relation type
ENSG00000164744	Chromatin interaction
ENSG00000183696	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1056663	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12702401	0.95[CEU][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13309127	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879833	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879834	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037483	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037485	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242478	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2686817	0.87[JPT][hapmap]
rs2686820	0.81[EUR][1000 genomes]
rs2686821	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2686823	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2686825	0.81[EUR][1000 genomes]
rs2686830	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686831	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686832	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686833	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686834	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686835	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686836	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686838	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2686839	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686840	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2686841	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686842	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708853	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708858	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708861	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708862	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708865	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708873	0.89[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2708875	0.84[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2708877	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708878	0.81[EUR][1000 genomes]
rs2708880	0.81[EUR][1000 genomes]
rs2708881	0.81[EUR][1000 genomes]
rs2708882	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708894	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708895	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708896	0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2708897	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708898	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708902	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708903	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708905	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708910	0.81[EUR][1000 genomes]
rs2708911	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2952720	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3176478	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3176564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34016848	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35151200	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35536957	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4720624	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs57995674	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60107343	0.81[EUR][1000 genomes]
rs885337	0.88[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs939904	0.89[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs939905	0.89[CEU][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs953572	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs953594	0.86[ASN][1000 genomes]
rs9648569	0.81[CEU][hapmap]

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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2242477	UPP1	cis	cerebellum	SCAN
rs2242477	ABCA13	cis	parietal	SCAN
rs2242477	PKD1L1	cis	parietal	SCAN
rs2242477	UPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2242477	POLM	cis	parietal	SCAN
rs2242477	PKD1L1	cis	cerebellum	SCAN
rs2242477	HUS1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47999600-48018000	Strong transcription	Fetal Thymus	thymus
2	chr7:48002000-48018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:48007400-48018200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:48009600-48018000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:48009800-48018000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:48010000-48018000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr7:48010200-48018200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:48010400-48018000	Strong transcription	Fetal Muscle Leg	muscle
9	chr7:48010400-48018200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:48010600-48018000	Strong transcription	Primary B cells from cord blood	blood
11	chr7:48010600-48018000	Strong transcription	Fetal Lung	lung
12	chr7:48010800-48018000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr7:48010800-48018000	Strong transcription	Placenta	Placenta
14	chr7:48010800-48018000	Strong transcription	Fetal Stomach	stomach
15	chr7:48010800-48018000	Strong transcription	Spleen	Spleen
16	chr7:48011000-48018000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:48011000-48018200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr7:48011200-48018000	Weak transcription	Right Atrium	heart
19	chr7:48011200-48018200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:48011800-48018000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:48011800-48018000	Strong transcription	HSMM	muscle
22	chr7:48012000-48018000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr7:48012000-48018200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:48012200-48018000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:48012400-48018000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:48012800-48018000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:48012800-48018000	Strong transcription	NHEK	skin
28	chr7:48013000-48018000	Strong transcription	Colonic Mucosa	Colon
29	chr7:48015200-48018200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:48015200-48018200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr7:48015600-48018000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:48015800-48018000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr7:48016200-48018200	Weak transcription	Aorta	Aorta
34	chr7:48016400-48018200	Weak transcription	Small Intestine	intestine
35	chr7:48016600-48018000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr7:48016600-48018000	Genic enhancers	Liver	Liver
37	chr7:48016800-48018000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr7:48016800-48018000	Genic enhancers	Adipose Nuclei	Adipose
39	chr7:48016800-48018200	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr7:48017000-48018000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:48017000-48018000	Weak transcription	Fetal Brain Female	brain
42	chr7:48017000-48018000	Weak transcription	Psoas Muscle	Psoas
43	chr7:48017000-48018200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:48017000-48018200	Weak transcription	Gastric	stomach
45	chr7:48017000-48018200	Weak transcription	Ovary	ovary
46	chr7:48017000-48018200	Weak transcription	Pancreas	Pancrea
47	chr7:48017200-48018000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:48017200-48018000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:48017200-48018000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:48017200-48018000	Weak transcription	Brain Germinal Matrix	brain

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