Variant report

Variant	rs3800960
Chromosome Location	chr7:99158402-99158403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99158028-99160221	GM12878	blood:	n/a	n/a
2	HEY1	chr7:99158037-99158522	K562	blood:	n/a	n/a
3	POLR2A	chr7:99158136-99158687	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99157952..99162241-chr7:99187776..99189560,3	K562	blood:
2	chr7:99062283..99063920-chr7:99156956..99159441,2	K562	blood:
3	chr7:99156838..99159123-chr7:99587844..99590431,2	K562	blood:
4	chr7:99148330..99152549-chr7:99153303..99160203,7	MCF-7	breast:
5	chr7:99068023..99071798-chr7:99154715..99160193,6	K562	blood:
6	chr7:99157018..99158552-chr7:99440966..99442480,2	K562	blood:
7	chr7:99158392..99160919-chr7:99272352..99275146,2	K562	blood:
8	chr7:99155790..99158631-chr7:99212983..99215798,6	K562	blood:

No data

Variant related genes	Relation type
FAM200A	TF binding region
ENSG00000235713	Chromatin interaction
ENSG00000197037	Chromatin interaction
ENSG00000241468	Chromatin interaction
ENSG00000198556	Chromatin interaction
ENSG00000248919	Chromatin interaction
ENSG00000221909	Chromatin interaction
ENSG00000106258	Chromatin interaction
ENSG00000106246	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1004387	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1011024	0.82[ASN][1000 genomes]
rs10211	0.81[JPT][hapmap]
rs10225314	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10238965	0.85[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10240199	0.93[ASN][1000 genomes]
rs10242455	0.83[JPT][hapmap]
rs10254729	0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10265385	0.98[ASN][1000 genomes]
rs10271049	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs10279308	0.94[YRI][hapmap]
rs10282706	0.81[JPT][hapmap]
rs1043466	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs10464604	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11539770	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11772470	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs11976018	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs12360	0.82[JPT][hapmap]
rs12538826	0.85[ASN][1000 genomes]
rs13240600	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1357319	0.82[JPT][hapmap]
rs1419745	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs15524	0.83[JPT][hapmap]
rs17161677	1.00[EUR][1000 genomes]
rs17161698	1.00[CEU][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17161766	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17161768	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17161769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17161771	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17161772	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17161774	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161780	1.00[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161783	0.82[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1851427	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1859690	0.83[JPT][hapmap]
rs1879859	0.82[JPT][hapmap]
rs1980307	0.85[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs1985453	1.00[ASW][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2003499	0.94[YRI][hapmap]
rs2037498	0.82[JPT][hapmap]
rs2037499	0.82[JPT][hapmap]
rs2057906	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2107705	1.00[EUR][1000 genomes]
rs2222411	0.82[JPT][hapmap]
rs2240384	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs2240385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2257401	0.82[JPT][hapmap]
rs2269985	1.00[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2272168	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2280600	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs2280601	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2404322	1.00[EUR][1000 genomes]
rs2404770	0.81[JPT][hapmap]
rs2687076	0.82[JPT][hapmap]
rs2687079	0.82[JPT][hapmap]
rs2687081	0.81[JPT][hapmap]
rs2687086	0.88[JPT][hapmap]
rs2687087	0.82[JPT][hapmap]
rs2687133	0.82[JPT][hapmap]
rs2687134	0.81[JPT][hapmap]
rs2687136	0.82[JPT][hapmap]
rs2687139	0.81[JPT][hapmap]
rs2687140	0.81[JPT][hapmap]
rs2687142	0.81[JPT][hapmap]
rs2687144	0.82[JPT][hapmap]
rs2687145	0.82[JPT][hapmap]
rs2740565	0.82[JPT][hapmap]
rs3137	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs34777615	0.85[ASN][1000 genomes]
rs3735453	0.82[JPT][hapmap]
rs3764815	1.00[CEU][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs3779354	0.90[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap]
rs3823812	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3843540	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs45442295	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45492098	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45540134	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45600842	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45622743	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4646446	0.82[ASW][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4646447	0.82[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4646449	0.82[ASW][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4646453	0.82[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4646456	0.82[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4646457	0.83[JPT][hapmap]
rs4646458	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs58024720	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58222677	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59986060	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60301933	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60865030	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61159815	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61337492	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61402640	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61543997	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6465750	0.82[JPT][hapmap]
rs6961634	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6962772	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs72494451	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72494452	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72494453	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72494454	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs776741	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs776746	0.82[JPT][hapmap]
rs7794705	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs7804551	0.80[ASN][1000 genomes]
rs7808022	0.83[JPT][hapmap]
rs8175345	0.82[ASW][hapmap]
rs868564	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs917154	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs940336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800960	BUD31	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99157400-99158600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr7:99157400-99158600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:99157400-99159400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr7:99157400-99159800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:99157400-99161400	Weak transcription	Ovary	ovary
6	chr7:99157400-99177400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:99157400-99177400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:99157600-99158600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:99157600-99158600	Genic enhancers	Rectal Smooth Muscle	rectum
10	chr7:99157600-99158800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
11	chr7:99157600-99159200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:99157600-99160000	Genic enhancers	Fetal Thymus	thymus
13	chr7:99157600-99160200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:99157600-99160800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
15	chr7:99157600-99162200	Genic enhancers	Placenta	Placenta
16	chr7:99157600-99164200	Weak transcription	Right Atrium	heart
17	chr7:99157800-99158600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
18	chr7:99157800-99158600	Genic enhancers	Duodenum Mucosa	Duodenum
19	chr7:99157800-99158800	Genic enhancers	Primary B cells from cord blood	blood
20	chr7:99157800-99158800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr7:99157800-99159200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
22	chr7:99157800-99159600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr7:99157800-99159800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:99157800-99159800	Genic enhancers	NHDF-Ad	bronchial
25	chr7:99157800-99160000	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr7:99157800-99160000	Genic enhancers	HSMM	muscle
27	chr7:99157800-99160800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:99157800-99161000	Genic enhancers	K562	blood
29	chr7:99157800-99161400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr7:99157800-99164800	Strong transcription	Primary T cells from cord blood	blood
31	chr7:99157800-99172200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr7:99157800-99172800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:99158000-99158600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:99158000-99158600	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr7:99158000-99158600	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr7:99158000-99158600	Genic enhancers	HSMMtube	muscle
37	chr7:99158000-99158800	Transcr. at gene 5' and 3'	NHLF	lung
38	chr7:99158000-99159000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr7:99158000-99159000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
40	chr7:99158000-99159400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:99158000-99159600	Genic enhancers	Lung	lung
42	chr7:99158000-99159800	Genic enhancers	Osteobl	bone
43	chr7:99158000-99160400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr7:99158000-99160600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:99158000-99160600	Transcr. at gene 5' and 3'	NHEK	skin
46	chr7:99158000-99162200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:99158000-99162600	Strong transcription	Fetal Kidney	kidney
48	chr7:99158000-99162800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr7:99158000-99162800	Strong transcription	Fetal Lung	lung
50	chr7:99158000-99164200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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