Variant report

Variant	rs9994689
Chromosome Location	chr4:3204565-3204566
allele	A/C
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	EBF1	chr4:3204522-3204908	GM12878	blood:	n/a	chr4:3204727-3204738
2	NFYB	chr4:3203993-3204590	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:3204472-3204958	GM12878	blood:	n/a	n/a
4	RCOR1	chr4:3203844-3204569	K562	blood:	n/a	n/a
5	MYC	chr4:3203568-3204573	NB4	blood:	n/a	n/a
6	NFIC	chr4:3203728-3204601	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:3204565-3204895	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:3203430-3205426	GM12891	blood:	n/a	n/a
9	SPI1	chr4:3204090-3204584	GM12891	blood:	n/a	n/a
10	RUNX3	chr4:3203665-3204573	GM12878	blood:	n/a	n/a
11	MAX	chr4:3203511-3204945	NB4	blood:	n/a	n/a
12	SPI1	chr4:3204073-3204617	HL-60	blood:	n/a	n/a
13	POLR2A	chr4:3203620-3205021	GM12892	blood:	n/a	n/a
14	MTA3	chr4:3203744-3204777	GM12878	blood:	n/a	n/a
15	TEAD4	chr4:3204140-3204821	K562	blood:	n/a	n/a
16	ATF2	chr4:3204107-3204572	GM12878	blood:	n/a	n/a
17	EBF1	chr4:3203866-3204935	GM12878	blood:	n/a	chr4:3204727-3204738
18	RUNX3	chr4:3203646-3204595	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
HTT	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10000252	0.93[EUR][1000 genomes]
rs10002065	0.93[EUR][1000 genomes]
rs10006977	0.80[EUR][1000 genomes]
rs10009229	0.93[EUR][1000 genomes]
rs10011127	0.93[EUR][1000 genomes]
rs10014333	0.80[EUR][1000 genomes]
rs10016755	0.93[EUR][1000 genomes]
rs10030079	0.93[EUR][1000 genomes]
rs10034313	0.87[EUR][1000 genomes]
rs10222986	0.80[EUR][1000 genomes]
rs1419036	0.93[EUR][1000 genomes]
rs16843857	0.93[EUR][1000 genomes]
rs16843866	0.93[EUR][1000 genomes]
rs16843869	0.93[EUR][1000 genomes]
rs28387056	0.87[EUR][1000 genomes]
rs28393280	0.87[EUR][1000 genomes]
rs28580164	0.93[EUR][1000 genomes]
rs28583552	0.90[EUR][1000 genomes]
rs28634516	0.93[EUR][1000 genomes]
rs28652828	0.84[EUR][1000 genomes]
rs28660254	0.93[EUR][1000 genomes]
rs28670335	0.87[EUR][1000 genomes]
rs28696693	0.81[EUR][1000 genomes]
rs28718346	0.80[EUR][1000 genomes]
rs28755900	0.84[EUR][1000 genomes]
rs3025836	1.00[EUR][1000 genomes]
rs363138	1.00[EUR][1000 genomes]
rs4346595	0.87[EUR][1000 genomes]
rs6830019	0.87[EUR][1000 genomes]
rs6835897	0.87[EUR][1000 genomes]
rs7436457	0.87[EUR][1000 genomes]
rs7664480	0.87[EUR][1000 genomes]
rs7693317	0.93[EUR][1000 genomes]
rs9995782	0.87[EUR][1000 genomes]
rs9996075	0.87[EUR][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	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
4	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr4:3181600-3206600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:3183400-3206800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:3185200-3208400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:3191200-3208600	Weak transcription	A549	lung
9	chr4:3191800-3207800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:3191800-3208200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:3191800-3211600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:3192800-3208600	Weak transcription	HUVEC	blood vessel
13	chr4:3193600-3204600	Weak transcription	Fetal Kidney	kidney
14	chr4:3193800-3206800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:3193800-3233000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:3194000-3206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:3194000-3237600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:3194200-3210600	Weak transcription	HMEC	breast
19	chr4:3194200-3212600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:3196000-3242600	Strong transcription	Fetal Intestine Small	intestine
21	chr4:3198800-3206200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr4:3199400-3208600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:3200400-3204600	Genic enhancers	Fetal Muscle Trunk	muscle
24	chr4:3201200-3206400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:3201400-3204600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:3201400-3205000	Enhancers	Psoas Muscle	Psoas
27	chr4:3201400-3207400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:3201400-3238400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:3201600-3206200	Enhancers	Fetal Lung	lung
30	chr4:3201800-3205000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:3202000-3205600	Enhancers	NHDF-Ad	bronchial
32	chr4:3202400-3205600	Strong transcription	Hela-S3	cervix
33	chr4:3202600-3204600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:3202600-3204600	Weak transcription	Gastric	stomach
35	chr4:3202600-3204800	Weak transcription	Colon Smooth Muscle	Colon
36	chr4:3202600-3205000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:3202600-3205000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:3202600-3205000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:3202600-3205000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr4:3202600-3206000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:3202600-3206800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:3202600-3207800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:3202600-3207800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:3202600-3207800	Weak transcription	Ovary	ovary
45	chr4:3202600-3208400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:3202800-3204600	Weak transcription	Adipose Nuclei	Adipose
47	chr4:3202800-3204600	Weak transcription	Colonic Mucosa	Colon
48	chr4:3202800-3205000	Weak transcription	Brain Hippocampus Middle	brain
49	chr4:3202800-3205200	Enhancers	Primary hematopoietic stem cells	blood
50	chr4:3202800-3205200	Enhancers	Fetal Thymus	thymus

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