Variant report

Variant	rs3798564
Chromosome Location	chr6:34358990-34358991
allele	C/G
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:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34203144..34206658-chr6:34358641..34361602,5	MCF-7	breast:
2	chr6:34346965..34349809-chr6:34357029..34359430,2	MCF-7	breast:
3	chr6:34336023..34338003-chr6:34357501..34359863,2	K562	blood:
4	chr6:34214133..34219385-chr6:34356600..34362053,16	K562	blood:
5	chr6:34202852..34208935-chr6:34358420..34361531,11	K562	blood:
6	chr6:34232571..34234778-chr6:34358274..34360439,2	K562	blood:
7	chr6:34242678..34244532-chr6:34357227..34359923,2	MCF-7	breast:
8	chr6:34202383..34217863-chr6:34357259..34364960,37	K562	blood:
9	chr6:34304154..34306840-chr6:34357586..34359775,2	MCF-7	breast:
10	chr6:34357967..34362826-chr6:34390808..34395314,8	K562	blood:
11	chr6:34213633..34219276-chr6:34358105..34363296,16	MCF-7	breast:
12	chr6:34358195..34361774-chr6:34391620..34393850,4	K562	blood:
13	chr6:34358377..34360251-chr6:34384641..34386602,2	MCF-7	breast:
14	chr6:34358853..34362255-chr6:34392162..34395391,9	MCF-7	breast:
15	chr6:34215295..34220270-chr6:34358417..34361933,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACSIN1-1	chr6:34355460-34360244	NONHSAT112133

No data

Variant related genes	Relation type
ENSG00000186577	Chromatin interaction
ENSG00000124614	Chromatin interaction
ENSG00000270800	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12662460	0.93[ASN][1000 genomes]
rs12664001	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12664016	0.84[ASN][1000 genomes]
rs12665397	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573905	1.00[CEU][hapmap]
rs16885998	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16889706	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16889714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs206921	0.81[JPT][hapmap]
rs206936	0.81[JPT][hapmap]
rs2071928	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28847046	0.88[ASN][1000 genomes]
rs34384951	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3778077	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3798562	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800476	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3800477	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4711390	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713766	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4713770	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713772	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713773	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713774	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713775	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713776	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713777	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4713780	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713781	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713783	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713784	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs4713787	0.84[AMR][1000 genomes]
rs58648597	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59310759	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60100381	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62399909	0.81[ASN][1000 genomes]
rs6909732	1.00[CEU][hapmap]
rs6924682	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6925243	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6935129	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7752035	0.87[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7767431	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7775635	0.88[ASN][1000 genomes]
rs9394200	1.00[CEU][hapmap]
rs9766229	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1034978	chr6:34327526-34362187	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv981324	chr6:34351435-34360764	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34337800-34359000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:34350600-34359000	Weak transcription	Esophagus	oesophagus
3	chr6:34354000-34359400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:34354000-34359600	Weak transcription	Small Intestine	intestine
5	chr6:34354800-34359000	Weak transcription	Lung	lung
6	chr6:34355000-34359000	Weak transcription	Pancreas	Pancrea
7	chr6:34355000-34359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:34357200-34359000	Weak transcription	Gastric	stomach
9	chr6:34358000-34359000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:34358000-34359000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:34358000-34359200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:34358000-34360800	Active TSS	HMEC	breast
13	chr6:34358000-34361000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:34358000-34361000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:34358000-34361200	Active TSS	NHLF	lung
16	chr6:34358200-34359000	Enhancers	Primary B cells from peripheral blood	blood
17	chr6:34358200-34359000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr6:34358200-34359200	Flanking Active TSS	HUVEC	blood vessel
19	chr6:34358200-34359600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:34358200-34359800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:34358200-34360800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:34358200-34361200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:34358200-34361400	Active TSS	Fetal Brain Female	brain
24	chr6:34358400-34359000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:34358400-34359000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:34358400-34359000	Flanking Active TSS	Fetal Stomach	stomach
27	chr6:34358400-34359000	Flanking Active TSS	NH-A	brain
28	chr6:34358400-34359200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr6:34358400-34359200	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr6:34358400-34359200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr6:34358400-34359200	Flanking Active TSS	Dnd41	blood
32	chr6:34358400-34359200	Flanking Active TSS	Osteobl	bone
33	chr6:34358400-34359400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr6:34358400-34359600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr6:34358400-34359600	Active TSS	Right Atrium	heart
36	chr6:34358400-34359600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:34358400-34359800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr6:34358400-34359800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:34358400-34360000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr6:34358400-34360800	Active TSS	Fetal Intestine Small	intestine
41	chr6:34358400-34361000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr6:34358400-34361000	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:34358400-34361000	Active TSS	A549	lung
44	chr6:34358400-34361200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr6:34358400-34361200	Active TSS	Aorta	Aorta
46	chr6:34358400-34361400	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:34358400-34361600	Active TSS	Brain Hippocampus Middle	brain
48	chr6:34358600-34359000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr6:34358600-34359000	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr6:34358600-34359000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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