Variant report

Variant	rs6690292
Chromosome Location	chr1:113188419-113188420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:113158924..113162270-chr1:113186808..113190181,3	K562	blood:
2	chr1:113178255..113183299-chr1:113188318..113192161,4	K562	blood:
3	chr1:113187333..113190054-chr1:113191408..113193923,3	K562	blood:
4	chr1:113187225..113191068-chr1:113200138..113202838,3	K562	blood:
5	chr1:113179962..113182760-chr1:113186932..113189454,2	MCF-7	breast:
6	chr1:113185385..113187833-chr1:113187867..113189719,2	K562	blood:
7	chr1:113167350..113169176-chr1:113187318..113189008,2	MCF-7	breast:
8	chr1:113160469..113163638-chr1:113186834..113189331,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap]
rs10745332	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857969	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102508	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102510	0.82[EUR][1000 genomes]
rs11102517	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12118370	0.91[ASN][1000 genomes]
rs12119489	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12125361	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126494	0.90[EUR][1000 genomes]
rs12136781	0.85[ASN][1000 genomes]
rs12137107	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12138335	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12143068	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1238	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12401734	1.00[CEU][hapmap]
rs12402469	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs12402929	0.94[CEU][hapmap]
rs12406906	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs12739994	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12750023	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12750621	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12758377	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17438324	0.90[ASN][1000 genomes]
rs2273369	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs2932529	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2932534	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932535	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932538	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932539	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3013433	0.94[EUR][1000 genomes]
rs3013441	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34531155	0.81[EUR][1000 genomes]
rs35482634	0.90[ASN][1000 genomes]
rs3762335	0.90[ASN][1000 genomes]
rs3790611	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs3790612	1.00[CEU][hapmap];0.85[ASN][1000 genomes]
rs3795820	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4240534	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4838960	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4838961	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61818800	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap]
rs6537742	0.81[CEU][hapmap]
rs6537744	1.00[CEU][hapmap];0.88[ASN][1000 genomes]
rs6537745	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537746	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6537747	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6658555	1.00[CEU][hapmap]
rs6659677	0.83[ASN][1000 genomes]
rs6661642	0.85[ASN][1000 genomes]
rs6663922	0.88[ASN][1000 genomes]
rs6668533	1.00[CEU][hapmap]
rs6671645	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672761	0.84[ASN][1000 genomes]
rs6673930	1.00[CEU][hapmap];0.90[ASN][1000 genomes]
rs6674053	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674068	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681371	1.00[CEU][hapmap]
rs6682678	0.83[CEU][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6690169	0.92[ASN][1000 genomes]
rs6691025	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691917	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6693880	0.90[ASN][1000 genomes]
rs6696991	0.86[ASN][1000 genomes]
rs6698030	0.81[EUR][1000 genomes]
rs6701351	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7415988	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7512984	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7516421	1.00[CEU][hapmap];0.85[ASN][1000 genomes]
rs7522110	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs7527076	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535636	1.00[CEU][hapmap];0.90[ASN][1000 genomes]
rs7537789	0.85[ASN][1000 genomes]
rs7542820	0.92[ASN][1000 genomes]
rs7546203	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7549547	0.85[ASN][1000 genomes]
rs7551933	1.00[CEU][hapmap];0.85[ASN][1000 genomes]
rs7552692	0.84[ASN][1000 genomes]
rs9429694	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9662162	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs999923	1.00[CEU][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
6	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6690292	ST7L	cis	Nerve Tibial	GTEx
rs6690292	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs6690292	ST7L	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113163600-113200000	Weak transcription	Fetal Kidney	kidney
2	chr1:113163800-113200200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:113163800-113200800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:113164000-113190000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:113164200-113204200	Weak transcription	Fetal Brain Male	brain
6	chr1:113168800-113189800	Weak transcription	Fetal Lung	lung
7	chr1:113168800-113191000	Weak transcription	Ovary	ovary
8	chr1:113168800-113199800	Weak transcription	Esophagus	oesophagus
9	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
10	chr1:113169000-113189800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:113169800-113188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:113172600-113191400	Weak transcription	Brain Germinal Matrix	brain
13	chr1:113174400-113190000	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:113175200-113188800	Weak transcription	Gastric	stomach
15	chr1:113175200-113189800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:113175200-113199800	Weak transcription	Psoas Muscle	Psoas
17	chr1:113175200-113200000	Weak transcription	Right Atrium	heart
18	chr1:113176000-113199200	Weak transcription	Fetal Brain Female	brain
19	chr1:113178200-113191400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:113179000-113215600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:113179400-113191400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:113179600-113197400	Weak transcription	Colonic Mucosa	Colon
23	chr1:113179800-113189800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:113179800-113191400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:113180000-113191400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:113180000-113193800	Weak transcription	Stomach Mucosa	stomach
27	chr1:113180000-113216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:113180200-113189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:113180200-113190000	Weak transcription	Liver	Liver
30	chr1:113180200-113190000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:113180200-113190400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:113180200-113191600	Weak transcription	NHLF	lung
33	chr1:113180200-113199800	Weak transcription	Spleen	Spleen
34	chr1:113180200-113200800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:113180200-113203000	Weak transcription	Aorta	Aorta
36	chr1:113180400-113190000	Weak transcription	NH-A	brain
37	chr1:113180400-113190200	Weak transcription	Adipose Nuclei	Adipose
38	chr1:113180400-113191000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:113180400-113191000	Weak transcription	Lung	lung
40	chr1:113180400-113193200	Weak transcription	HSMMtube	muscle
41	chr1:113180600-113188800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:113180800-113189400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:113180800-113189600	Weak transcription	Osteobl	bone
44	chr1:113180800-113189800	Weak transcription	NHDF-Ad	bronchial
45	chr1:113180800-113190000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:113180800-113190800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:113180800-113191400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:113180800-113191600	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:113180800-113200000	Weak transcription	Brain Anterior Caudate	brain
50	chr1:113181000-113190000	Weak transcription	Rectal Mucosa Donor 31	rectum

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