Variant report

Variant	rs40102
Chromosome Location	chr5:115814496-115814497
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:115814243-115814528	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr5:115814261-115814611	SK-N-SH_RA	brain:	n/a	n/a
3	TCF12	chr5:115814188-115814686	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr5:115814163-115814637	SK-N-SH	brain:	n/a	chr5:115814436-115814443 chr5:115814432-115814448 chr5:115814429-115814450 chr5:115814433-115814443 chr5:115814436-115814443 chr5:115814435-115814445 chr5:115814436-115814443
5	TEAD4	chr5:115814143-115814604	K562	blood:	n/a	n/a
6	PBX3	chr5:115814213-115814573	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr5:115814461-115817704	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:115814296-115814736	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:115814059-115818431	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SEMA6A	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10058506	0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs11241394	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs153742	0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap]
rs153743	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs154555	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs171797	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs191732	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278262	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs258017	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs258018	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs258020	0.94[ASN][1000 genomes]
rs26591	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs26594	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs27495	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27644	0.89[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs28028	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28029	0.88[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs28308	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34967	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40000	0.87[AFR][1000 genomes]
rs469035	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115783600-115829600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:115791600-115838000	Weak transcription	Right Ventricle	heart
3	chr5:115796000-115833400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:115797000-115834800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:115797000-115838400	Strong transcription	Placenta	Placenta
6	chr5:115797400-115833800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:115797600-115834600	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr5:115797800-115834800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:115798000-115833200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:115798000-115834600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:115799000-115830400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:115799400-115832000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr5:115801400-115824000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:115801400-115825000	Weak transcription	Psoas Muscle	Psoas
15	chr5:115803000-115815400	Weak transcription	Thymus	Thymus
16	chr5:115803400-115816000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:115803400-115833200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:115804600-115822600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:115808800-115818200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:115810800-115821200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:115811000-115814800	Strong transcription	Colon Smooth Muscle	Colon
22	chr5:115811000-115815600	Strong transcription	Left Ventricle	heart
23	chr5:115811800-115814600	Strong transcription	Rectal Smooth Muscle	rectum
24	chr5:115811800-115818200	Strong transcription	Fetal Brain Female	brain
25	chr5:115812000-115816000	Strong transcription	Brain Anterior Caudate	brain
26	chr5:115812200-115814800	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr5:115812200-115817200	Strong transcription	Brain Substantia Nigra	brain
28	chr5:115812200-115818400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:115812600-115815800	Strong transcription	Brain Angular Gyrus	brain
30	chr5:115812600-115815800	Strong transcription	Brain Hippocampus Middle	brain
31	chr5:115812600-115818600	Strong transcription	Colonic Mucosa	Colon
32	chr5:115813200-115815800	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr5:115813200-115816000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:115813200-115818400	Strong transcription	Brain Germinal Matrix	brain
35	chr5:115813200-115819200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:115813200-115824400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:115813200-115826200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:115813400-115815800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:115813400-115816400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:115813400-115816400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:115813400-115818400	Strong transcription	Fetal Kidney	kidney
42	chr5:115813400-115820800	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr5:115813400-115822400	Strong transcription	Fetal Intestine Large	intestine
44	chr5:115813600-115814600	Genic enhancers	Fetal Lung	lung
45	chr5:115813600-115815000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr5:115813600-115815800	Weak transcription	Spleen	Spleen
47	chr5:115813600-115816000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:115813600-115816400	Enhancers	Primary hematopoietic stem cells	blood
49	chr5:115813600-115818000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr5:115813600-115821400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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