Variant report

Variant	rs6704413
Chromosome Location	chr1:173902723-173902724
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173829730..173832561-chr1:173902531..173906389,3	MCF-7	breast:
2	chr1:173834207..173835952-chr1:173901003..173903203,2	K562	blood:
3	chr1:173901657..173903575-chr1:173991389..173993213,2	K562	blood:
4	chr1:173839047..173840684-chr1:173900730..173903519,2	K562	blood:
5	chr1:173836510..173838648-chr1:173900344..173902921,2	K562	blood:
6	chr1:173833906..173839819-chr1:173898429..173906150,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RC3H1-2	chr1:173900352-173905313	NONHSAT007713

No data

Variant related genes	Relation type
ENSG00000135870	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000270084	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1322769	1.00[AMR][1000 genomes]
rs16846397	1.00[AMR][1000 genomes]
rs16846483	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2227620	1.00[AMR][1000 genomes]
rs57006357	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57343517	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58576036	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58930477	1.00[AMR][1000 genomes]
rs59355797	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59846661	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6667627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025612	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025620	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027407	1.00[AMR][1000 genomes]
rs73027443	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027460	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027463	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027464	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027488	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73035116	1.00[AMR][1000 genomes]
rs73035134	1.00[AMR][1000 genomes]
rs73035139	1.00[AMR][1000 genomes]
rs73037076	1.00[AMR][1000 genomes]
rs73037083	1.00[AMR][1000 genomes]
rs73037097	1.00[AMR][1000 genomes]
rs73041050	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73041059	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7519571	1.00[AMR][1000 genomes]
rs7531236	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7547873	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9726181	1.00[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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
3	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv3407396	chr1:173896346-173917122	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
3	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
4	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:173893400-173908400	Weak transcription	Colonic Mucosa	Colon
6	chr1:173894000-173904800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:173894400-173905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:173894600-173907800	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:173894600-173914400	Weak transcription	Right Ventricle	heart
10	chr1:173895000-173903400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:173895200-173912200	Weak transcription	Stomach Mucosa	stomach
12	chr1:173895400-173907600	Weak transcription	Ovary	ovary
13	chr1:173895600-173906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:173895800-173906200	Weak transcription	HepG2	liver
15	chr1:173896400-173902800	Weak transcription	Brain Anterior Caudate	brain
16	chr1:173896400-173907800	Weak transcription	Gastric	stomach
17	chr1:173896400-173910000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:173896400-173914400	Weak transcription	Pancreas	Pancrea
19	chr1:173896600-173902800	Weak transcription	Adipose Nuclei	Adipose
20	chr1:173896800-173908400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:173897000-173907800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:173897000-173908400	Weak transcription	Fetal Intestine Small	intestine
23	chr1:173897400-173907200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:173897600-173903600	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:173897600-173907200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:173897800-173907600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:173898000-173903200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr1:173898000-173903400	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:173898000-173907800	Weak transcription	Fetal Stomach	stomach
30	chr1:173898000-173915200	Weak transcription	Aorta	Aorta
31	chr1:173898200-173903600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:173898200-173904800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:173898200-173907800	Weak transcription	Thymus	Thymus
34	chr1:173898200-173908800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:173898200-173910000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:173898200-173910200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:173898200-173912200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:173898400-173903600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:173898400-173907200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:173898600-173905400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:173898600-173906200	Weak transcription	Fetal Kidney	kidney
42	chr1:173898600-173906800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:173898800-173903000	Weak transcription	Primary B cells from cord blood	blood
44	chr1:173898800-173907400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:173898800-173912200	Weak transcription	NHEK	skin
46	chr1:173899000-173903400	Weak transcription	Fetal Thymus	thymus
47	chr1:173899000-173906400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:173899200-173903400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:173899200-173913800	Weak transcription	Fetal Heart	heart
50	chr1:173899400-173903600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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