Variant report

Variant	rs3025828
Chromosome Location	chr4:3199919-3199920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:3199880-3200030	GM12866	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:3196534..3198445-chr4:3199145..3202681,3	MCF-7	breast:
2	chr4:3198767..3201589-chr4:3205196..3207411,2	K562	blood:
3	chr4:3196724..3198622-chr4:3198822..3201545,2	MCF-7	breast:

Variant related genes	Relation type
HTT	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3025842	1.00[AFR][1000 genomes]
rs362326	0.94[AFR][1000 genomes]
rs362330	0.85[YRI][hapmap]
rs363077	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs363115	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs363122	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs363132	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active 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	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
7	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr4:3173600-3200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:3174000-3204000	Strong transcription	Stomach Smooth Muscle	stomach
12	chr4:3178800-3200000	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:3181000-3201400	Weak transcription	Hela-S3	cervix
14	chr4:3181600-3206600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:3182400-3203200	Strong transcription	Fetal Intestine Large	intestine
16	chr4:3183000-3202600	Strong transcription	Liver	Liver
17	chr4:3183400-3206800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:3185200-3208400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:3190600-3203600	Weak transcription	Small Intestine	intestine
20	chr4:3191200-3201400	Weak transcription	Psoas Muscle	Psoas
21	chr4:3191200-3201400	Weak transcription	NHDF-Ad	bronchial
22	chr4:3191200-3203400	Weak transcription	Fetal Heart	heart
23	chr4:3191200-3208600	Weak transcription	A549	lung
24	chr4:3191600-3201400	Weak transcription	NH-A	brain
25	chr4:3191600-3203600	Weak transcription	K562	blood
26	chr4:3191800-3207800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:3191800-3208200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:3191800-3211600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:3192000-3201400	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:3192800-3201800	Strong transcription	Adipose Nuclei	Adipose
31	chr4:3192800-3208600	Weak transcription	HUVEC	blood vessel
32	chr4:3193600-3204600	Weak transcription	Fetal Kidney	kidney
33	chr4:3193800-3203200	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:3193800-3206800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:3193800-3233000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:3194000-3200400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr4:3194000-3202000	Strong transcription	Esophagus	oesophagus
38	chr4:3194000-3202600	Strong transcription	Gastric	stomach
39	chr4:3194000-3202600	Strong transcription	Lung	lung
40	chr4:3194000-3203600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:3194000-3206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:3194000-3237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:3194200-3203200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:3194200-3210600	Weak transcription	HMEC	breast
45	chr4:3194200-3212600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:3194400-3200000	Strong transcription	HSMM	muscle
47	chr4:3194400-3201200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:3194400-3201600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:3194400-3203000	Strong transcription	GM12878-XiMat	blood
50	chr4:3194600-3203000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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