Variant report

Variant	rs6702168
Chromosome Location	chr1:70677818-70677819
allele	A/C
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70674826..70679166-chr1:70682889..70688598,11	K562	blood:
2	chr1:70677689..70679328-chr1:70679670..70681328,2	K562	blood:
3	chr1:70676208..70679371-chr1:70691028..70694933,4	K562	blood:
4	chr1:70670145..70673365-chr1:70675136..70679229,4	K562	blood:
5	chr1:70677362..70679072-chr1:70694969..70697768,2	K562	blood:
6	chr1:70670740..70673144-chr1:70677061..70678983,2	MCF-7	breast:
7	chr1:70675754..70677274-chr1:70677363..70679421,2	K562	blood:
8	chr1:70677380..70678950-chr1:70685516..70687818,2	MCF-7	breast:
9	chr1:70676847..70678967-chr1:70704287..70707286,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228988	Chromatin interaction
ENSG00000066557	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10489927	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489928	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562802	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566666	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131235	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131251	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034756	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2210545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2478801	0.89[AMR][1000 genomes]
rs34821575	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35262515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753817	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767206	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767207	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767208	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41488747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs4649913	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650031	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55727788	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56902977	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639674	0.86[ASN][1000 genomes]
rs58696538	0.85[EUR][1000 genomes]
rs58927829	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59234513	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60272091	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60441970	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs632517	1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs655588	0.85[AMR][1000 genomes]
rs668525	1.00[MEX][hapmap];0.94[AMR][1000 genomes]
rs716240	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74085992	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085996	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085999	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74088004	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088016	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088024	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088029	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74088032	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74088035	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088042	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7533067	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6702168	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70672000-70686200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:70672000-70687000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:70672400-70681200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:70672400-70686800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:70672600-70686400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:70672600-70686600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:70672800-70686600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:70673000-70680800	Weak transcription	Esophagus	oesophagus
9	chr1:70673000-70680800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:70673000-70681800	Weak transcription	Fetal Kidney	kidney
11	chr1:70673000-70683400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:70673200-70678800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:70673200-70680800	Weak transcription	Fetal Intestine Large	intestine
14	chr1:70673200-70686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:70673200-70686200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:70673200-70686400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:70673200-70686400	Weak transcription	HSMMtube	muscle
18	chr1:70673200-70686600	Weak transcription	NH-A	brain
19	chr1:70673400-70686200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:70673400-70686200	Weak transcription	HMEC	breast
21	chr1:70673400-70686400	Weak transcription	Fetal Brain Male	brain
22	chr1:70673400-70686600	Weak transcription	A549	lung
23	chr1:70673600-70686400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:70673800-70680800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:70673800-70681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:70673800-70686000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:70673800-70686600	Weak transcription	Brain Hippocampus Middle	brain
28	chr1:70673800-70687200	Weak transcription	Small Intestine	intestine
29	chr1:70674200-70681000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:70674200-70681400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:70674200-70685800	Weak transcription	Right Ventricle	heart
32	chr1:70674200-70686600	Weak transcription	Brain Angular Gyrus	brain
33	chr1:70674200-70686600	Weak transcription	Brain Anterior Caudate	brain
34	chr1:70674200-70686800	Weak transcription	Aorta	Aorta
35	chr1:70674400-70679600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:70674400-70680600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:70674400-70680600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:70674400-70680600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:70674400-70680800	Weak transcription	Primary T cells from cord blood	blood
40	chr1:70674400-70680800	Weak transcription	Fetal Thymus	thymus
41	chr1:70674400-70680800	Weak transcription	Thymus	Thymus
42	chr1:70674400-70681000	Weak transcription	Fetal Brain Female	brain
43	chr1:70674400-70681000	Weak transcription	Fetal Lung	lung
44	chr1:70674400-70681000	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:70674400-70681200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:70674400-70686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:70674400-70686400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:70674400-70686600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:70674400-70686600	Weak transcription	Colonic Mucosa	Colon
50	chr1:70674400-70686600	Weak transcription	Colon Smooth Muscle	Colon

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