Variant report

Variant	rs6691488
Chromosome Location	chr1:213262458-213262459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213255405..213259890-chr1:213260216..213264624,5	K562	blood:
2	chr1:213243830..213246340-chr1:213261615..213263124,2	K562	blood:
3	chr1:213257126..213258627-chr1:213261008..213263824,2	K562	blood:

Variant related genes	Relation type
ENSG00000136643	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10127851	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10465694	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10864034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864036	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10864038	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11120082	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1391549	0.85[AMR][1000 genomes]
rs1391550	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1498357	0.86[AMR][1000 genomes]
rs1566247	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1566248	0.84[EUR][1000 genomes]
rs17020338	0.82[AMR][1000 genomes]
rs1976333	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1995151	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes]
rs2132428	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs2172982	0.81[AMR][1000 genomes]
rs2173398	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2494767	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs2647387	0.86[AMR][1000 genomes]
rs2817976	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2817978	0.86[AMR][1000 genomes]
rs2817981	0.86[AMR][1000 genomes]
rs2817984	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2841427	0.85[AMR][1000 genomes]
rs2841439	0.86[AMR][1000 genomes]
rs2935219	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2936011	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3002285	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3010779	0.95[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs3010780	0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs3010787	0.84[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3010789	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3124668	0.84[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4543872	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4655386	0.82[AMR][1000 genomes]
rs4951475	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4951476	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951478	0.83[EUR][1000 genomes]
rs4951479	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951662	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4951677	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6419470	0.83[AMR][1000 genomes]
rs6540774	0.83[EUR][1000 genomes]
rs6540776	0.84[EUR][1000 genomes]
rs6540778	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6540780	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540781	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6540782	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6657234	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6658259	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6666814	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670025	0.87[ASN][1000 genomes]
rs6671872	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6679510	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6692056	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692144	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6693291	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6697921	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6699158	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700169	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7535369	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7547274	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9308430	0.83[AMR][1000 genomes]
rs9429901	0.82[AMR][1000 genomes]
rs9429902	0.82[AMR][1000 genomes]
rs9430118	0.83[AMR][1000 genomes]
rs9430120	0.81[AMR][1000 genomes]
rs9430121	0.82[AMR][1000 genomes]
rs9430122	0.81[AMR][1000 genomes]
rs9430123	0.84[AMR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6691488	KCNH1	cis	cerebellum	SCAN
rs6691488	SNORA16B	cis	cerebellum	SCAN
rs6691488	ANGEL2	cis	cerebellum	SCAN
rs6691488	ANGEL2	cis	parietal	SCAN
rs6691488	RPS6KC1	cis	Artery Tibial	GTEx
rs6691488	BATF3	cis	parietal	SCAN
rs6691488	ANGEL2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213228800-213263200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:213229400-213283400	Weak transcription	Hela-S3	cervix
3	chr1:213233000-213262600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:213240200-213272600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:213240400-213274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:213243800-213262600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:213244200-213268000	Weak transcription	Brain Substantia Nigra	brain
8	chr1:213244200-213271000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:213244200-213273200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:213244200-213273200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:213244200-213296200	Weak transcription	NHDF-Ad	bronchial
12	chr1:213246800-213283800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:213251200-213293000	Weak transcription	NH-A	brain
14	chr1:213251400-213263800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:213251600-213272000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:213252400-213264400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:213252600-213297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:213252800-213263600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:213253000-213263000	Weak transcription	Colonic Mucosa	Colon
20	chr1:213253000-213263200	Weak transcription	Thymus	Thymus
21	chr1:213253000-213271200	Weak transcription	Small Intestine	intestine
22	chr1:213253200-213262800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:213253200-213275600	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:213253200-213277600	Weak transcription	Gastric	stomach
25	chr1:213253600-213262800	Strong transcription	Adipose Nuclei	Adipose
26	chr1:213254800-213297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:213255200-213264800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:213255200-213266000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:213255200-213270800	Weak transcription	GM12878-XiMat	blood
30	chr1:213255200-213273400	Weak transcription	Fetal Brain Male	brain
31	chr1:213255200-213279400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:213255400-213267200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:213255400-213270400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:213255600-213263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:213255600-213271800	Weak transcription	Right Ventricle	heart
36	chr1:213256600-213262600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:213256800-213262600	Strong transcription	Primary B cells from cord blood	blood
38	chr1:213256800-213263000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:213256800-213284000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:213257000-213262600	Weak transcription	NHEK	skin
41	chr1:213257000-213262800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:213257200-213262600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:213258400-213280600	Weak transcription	A549	lung
44	chr1:213258600-213262800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:213258600-213267200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:213258600-213271000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr1:213258600-213277400	Weak transcription	Psoas Muscle	Psoas
48	chr1:213258800-213284200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:213259200-213265200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:213259400-213262800	Strong transcription	HepG2	liver

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