Variant report

Variant	rs3087804
Chromosome Location	chr15:83685773-83685774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83684589..83686265-chr15:83730370..83733896,3	K562	blood:
2	chr15:83679205..83686226-chr15:83733349..83739878,12	K562	blood:
3	chr15:83685645..83690096-chr15:83691641..83694486,5	MCF-7	breast:
4	chr15:83684703..83687598-chr15:83730655..83733296,2	K562	blood:
5	chr15:83684576..83687517-chr15:83693136..83695627,2	K562	blood:

Variant related genes	Relation type
ENSG00000263643	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000259767	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10400812	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520576	1.00[JPT][hapmap]
rs1112404	1.00[JPT][hapmap]
rs11259965	1.00[JPT][hapmap]
rs11259969	1.00[JPT][hapmap]
rs11852408	1.00[JPT][hapmap]
rs11852496	1.00[JPT][hapmap]
rs11853742	0.91[JPT][hapmap]
rs11856171	1.00[JPT][hapmap]
rs11857641	1.00[JPT][hapmap]
rs11858074	0.95[ASN][1000 genomes]
rs11858377	1.00[JPT][hapmap]
rs12439782	0.87[EUR][1000 genomes]
rs12440386	1.00[JPT][hapmap]
rs12441585	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs12443109	1.00[JPT][hapmap]
rs12591855	1.00[JPT][hapmap]
rs12592391	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12593316	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12593638	0.91[JPT][hapmap]
rs12594496	1.00[JPT][hapmap]
rs12595330	1.00[JPT][hapmap]
rs12899522	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900411	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12901811	0.95[ASN][1000 genomes]
rs12902721	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12903066	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12904695	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906027	0.95[ASN][1000 genomes]
rs12906626	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907032	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911706	0.95[ASN][1000 genomes]
rs12911891	0.95[ASN][1000 genomes]
rs12913130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917594	0.94[ASN][1000 genomes]
rs13329195	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329269	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17158080	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs17158127	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17294476	0.90[JPT][hapmap]
rs17507300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17567151	1.00[JPT][hapmap]
rs17567869	1.00[JPT][hapmap]
rs17568459	1.00[JPT][hapmap]
rs2034617	0.91[JPT][hapmap]
rs2034618	1.00[JPT][hapmap]
rs2084839	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2381030	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28436027	0.91[JPT][hapmap]
rs28485801	0.97[ASN][1000 genomes]
rs28580677	0.97[ASN][1000 genomes]
rs34869943	0.92[ASN][1000 genomes]
rs35207081	0.95[ASN][1000 genomes]
rs35627116	0.94[ASN][1000 genomes]
rs36038412	0.95[ASN][1000 genomes]
rs4079029	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4563011	1.00[JPT][hapmap]
rs61375537	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6603044	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603046	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6603047	0.91[JPT][hapmap]
rs66606849	0.95[ASN][1000 genomes]
rs67482297	0.95[ASN][1000 genomes]
rs67822554	0.95[ASN][1000 genomes]
rs7163516	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164083	0.82[JPT][hapmap]
rs7165114	1.00[JPT][hapmap]
rs7165978	1.00[JPT][hapmap]
rs7166645	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7170547	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172665	0.96[CEU][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7177599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181169	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	1.00[JPT][hapmap]
rs750214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8023669	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs8027193	1.00[JPT][hapmap]
rs8027577	1.00[JPT][hapmap]
rs8031896	0.98[ASN][1000 genomes]
rs8035810	1.00[JPT][hapmap]
rs8037783	1.00[JPT][hapmap]
rs8038486	1.00[JPT][hapmap]
rs8040457	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040998	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8043224	1.00[JPT][hapmap]
rs9646239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs965264	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3087804	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs3087804	WHAMM	cis	cerebellum	SCAN
rs3087804	BTBD1	cis	Nerve Tibial	GTEx
rs3087804	BTBD1	cis	parietal	SCAN
rs3087804	TM6SF1	cis	cerebellum	SCAN
rs3087804	ARNT2	cis	cerebellum	SCAN
rs3087804	WHAMM	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83680800-83688800	Weak transcription	Aorta	Aorta
2	chr15:83681000-83700200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:83681000-83705000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:83681200-83686000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:83681200-83687400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:83681200-83688800	Weak transcription	Psoas Muscle	Psoas
7	chr15:83681200-83693400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:83681200-83698200	Weak transcription	NHLF	lung
9	chr15:83681200-83710200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:83681400-83685800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:83681400-83685800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:83681400-83685800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:83681400-83685800	Weak transcription	Liver	Liver
14	chr15:83681400-83685800	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:83681400-83685800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:83681400-83685800	Weak transcription	Placenta	Placenta
17	chr15:83681400-83685800	Weak transcription	NH-A	brain
18	chr15:83681400-83687200	Weak transcription	Colonic Mucosa	Colon
19	chr15:83681400-83698000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:83681400-83698400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:83681600-83685800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:83681600-83685800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:83681600-83685800	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:83681600-83685800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:83681600-83685800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:83681600-83685800	Weak transcription	HSMMtube	muscle
27	chr15:83681600-83685800	Weak transcription	NHEK	skin
28	chr15:83681600-83685800	Weak transcription	Osteobl	bone
29	chr15:83681600-83686800	Weak transcription	Brain Substantia Nigra	brain
30	chr15:83681600-83687200	Weak transcription	Brain Angular Gyrus	brain
31	chr15:83681600-83687200	Weak transcription	Small Intestine	intestine
32	chr15:83681600-83687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:83681600-83688800	Weak transcription	Brain Anterior Caudate	brain
34	chr15:83681600-83688800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:83681600-83698200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:83681600-83698200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
38	chr15:83681800-83685800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:83681800-83687200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:83681800-83687200	Weak transcription	HepG2	liver
41	chr15:83681800-83687400	Weak transcription	Fetal Stomach	stomach
42	chr15:83681800-83687400	Weak transcription	Right Ventricle	heart
43	chr15:83681800-83689000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:83682000-83685800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:83682000-83685800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:83682000-83685800	Weak transcription	Fetal Lung	lung
47	chr15:83682000-83687200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr15:83682000-83687200	Weak transcription	Thymus	Thymus
49	chr15:83682000-83688800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr15:83682000-83688800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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